As the Portuguese hosts hailed a "new chapter" in relations, Senegal's president railed against new EU-African trade deals proposed by the EU.
And Zimbabwe's President Robert Mugabe reportedly accused Europe of arrogance in criticising his human rights record.
The hosts have lauded the summit as heralding a new relationship of equals.
The 67 leaders gathered at the summit agreed to work together to forge a new partnership on issues including security, development, trade and good governance.
The BBC's Mark Doyle, in Lisbon, says the joint declaration is hugely ambitious in scope, and that clear differences remain on several issues.
Fragile economies
Angry words flew over trade deals - known as Economic Partnership Agreements - proposed to replace existing agreements due to expire at the end of the year.
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Although some east African nations have already agreed to the deals, many other countries argue that they will damage their fragile economies.
The deals - to replace historical agreements which gave former European colonies preferential trade terms - demand that African countries open their markets to European goods in order to keep tariff-free EU access for their own exports.
The summit was seen as an EU attempt regain lost ground in Africa and combat growing Chinese influence in the continent.
But President Wade said that "Europe is close to losing the battle of competition in Africa".
Our correspondent says that while China has massively increased its investments in Africa, it does not tend to comment on issues such as democracy and human rights.
'Arrogance'
The point was evidenced by tensions over the presence of Mr Mugabe, widely criticised for human rights abuses and economic mismanagement in Zimbabwe.
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On Sunday Mr Mugabe was reported to have lambasted four EU countries for "arrogance" in their criticisms, according to a copy of a speech at a closed meeting obtained by French news agency AFP.
His comments came in response to German Chancellor Angela Merkel's earlier assertion that his policies had "damaged Africa".
"It is important that people keep in mind that Africans fought for human rights from oppressive rule," said Mr Mugabe, who is regarded by many African leaders as the heroic liberator of Zimbabwe.
The meeting was the first EU-African summit for seven years. Previous attempts had collapsed over the question of Mr Mugabe's attendance.
Portuguese PM Jose Socrates, who earlier lauded the gathering as a "summit of equals", said it was an achievement in itself that the meeting had taken place.
Most members want to issue a strong statement ahead of next month's UN talks on a new deal to cut CO2 gases - replacing the Kyoto protocol.
But the 53-member group is yet to reach a consensus on the issue, amid reported opposition from Canada and Australia.
Meanwhile, India's Kamalesh Sharma has been appointed secretary general. He will replace Don McKinnon.
Mr McKinnon, a New Zealander, is stepping down at the end of his four-year term.
The first day of the summit was marred by violent clashes between protesters and police in Uganda's capital, Kampala.
Protesters denounced Britain's Queen Elizabeth for meeting Ugandan President Yoweri Museveni, who they say abuses rights.
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 We really have to get a concerted view on this (climate change) with the Bali conference coming up  Don McKinnon, Commonwealth Secretary General
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The three-day summit on Friday suspended Pakistan for civil rights violations under its emergency rule.
Opposition
On Saturday, the Commonwealth leaders are working at a retreat on Lake Victoria, away from officials and media.
Officials said the summit would try to iron out differences between member states on climate change.
Many Commonwealth nations, led by Britain, want to issue an influential statement before next month's UN talks in Bali, which will discuss a new agreement to replace the Kyoto protocol, which expires in 2012.
"We really have to get a concerted view on this (climate change) with the Bali conference coming up," Mr McKinnon said on Friday.
But Canada has insisted that any statement should refer to the need for contributions from the world's major polluters, including the United States, who has so far resisted any binding targets.
Australia is also a major CO2 emitter and - like the US - has not ratified the Kyoto Protocol.
Brown optimism
A new global trade agreement is also on the summit's agenda.
It is one of the most divisive issues for the Commonwealth, which includes some of the world's wealthiest nations as well as some of the poorest.
UK Prime Minister Gordon Brown on Saturday expressed optimism that a new deal could be reached in the next few weeks.
The talks have repeatedly stalled since their inception in Qatar's capital, Doha, in 2001.
Those illegally sharing files will face the loss of their net access thanks to a newly-created anti-piracy body granted the wide-ranging powers.
The anti-piracy body comes out of a deal agreed by France's music and movie makers and its net firms.
The group who brokered the deal said the measures were intended to curb casual piracy rather than tackle large scale pirate groups.
French President Nicolas Sarkozy said the deal was a "decisive moment for the future of a civilised internet".
Net firms will monitor what their customers are doing and pass on information about persistent pirates to the new independent body. Those identified will get a warning and then be threatened with either being cut off or suspended if they do not stop illegal file-sharing.
The agreement between net firms, record companies, film-makers and government was drawn up by a special committee created to look at the problem of the net and cultural protection.
Denis Olivennes, head of the French chain store FNAC, who chaired the committee said current penalties for piracy - large fines and years in jail - were "totally disproportionate" for those young people who do file-share illegally.
In return for agreeing to monitor net use, film-makers agreed to speed up the transfer of movies to DVD and music firms pledged to support DRM-free tracks on music stores.
The deal was hailed by the International Federation of the Phonographic Industry (IFPI), which represents the global interests of the music business.
"This is the single most important initiative to help win the war on online piracy that we have seen so far," it said in a statement.
French consumer group UFC Que Choisir was more cautious.
It said the agreement was "very tough, potentially destructive of freedom, anti-economic and against digital history".
Mr Tusk said the decision was out of respect for a deal negotiated by the previous conservative government.
But he promised to pursue a more pro-European Union policy, saying his government would ensure that "Poles and Poland are quickly ready for the euro".
Mr Tusk also confirmed Poland would pull its troops out of Iraq next year.
Poland currently has 900 soldiers serving in Iraq and the prime minister said the decision to pull them out had been taken because of its importance for Polish public opinion.
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We have fulfilled - and even more than fulfilled - our commitments to our allies Donald Tusk
Polish Prime Minister |
In campaigning for last month's election, his party, Civic Platform, had promised to bring the troops home.
"We are going to carry out this withdrawal in the knowledge that we have fulfilled - and even more than fulfilled - our commitments to our allies," he said.
In 2003, 2,600 Polish troops took part in the invasion of Iraq and led a force in the south-central area of the country.
The president, Lech Kaczynski, is commander of the armed forces and opposes withdrawal but does not have the power to challenge the government.
Charter objections
Before Mr Tusk's party came to power, the previous government led by the president's twin, Jaroslaw Kaczynski, announced that Poland would join Britain in opting out of the Charter of Fundamental Rights.
The document features in the EU Reform Treaty as no more than a short reference but Mr Kaczynski's coalition was concerned that some of the charter's provisions relating to moral and family issues could contradict Polish law.
There was particular concern about same-sex marriages which are legal in a number of EU member states.
The new government has no such objection and the prime minister told the Polish parliament that his party and its coalition ally, the Peasants' Party, were in favour of signing up to it.
But Mr Tusk told MPs that the opt-out would remain because he needed the support of Jaroslaw Kaczynski's party in order to reach the two-thirds majority required to ratify the Reform Treaty as a whole.
"Our European Union partners understand our situation," he said.
His three-hour speech in the Sejm (the lower house of parliament) is believed to be the longest ever given by a democratically-elected prime minister in Poland.
The army engineers arrived on Saturday to prepare for a joint UN and African Union peacekeeping force of 26,000.
The key Justice and Equality Movement (Jem) rebel group accuses China of being complicit in the Darfur conflict.
Last month the group attacked a Chinese-controlled oilfield, kidnapping several workers.
The Jem says it wants China to withdraw its support for the Sudanese government.
They say that oil sold to the Chinese is being used to fund government operations in Darfur.
Rebels would not allow the Chinese into areas controlled by their forces, Jem leader Khalil Ibrahim told the news agency Reuters following the arrival of the engineers.
'Oil for blood'
"We oppose them coming because China is not interested in human rights. It is just interested in Sudan's resources," he said.
"We are calling on them to quit Sudan, especially the petroleum areas."
Mr Ibrahim did not say whether he would target the Chinese engineers.
"I am not saying I will attack them. I will not say I will not attack them," he said.
"What I am saying is that they are taking our oil for blood."
The Chinese engineers are tasked with building roads and bridges and dig wells ahead of the deployment of the joint peacekeeping force planned for January.
The rebels have said they would not object to peacekeepers from any country other than China.
But on Friday, Sudanese President Omar Al-Bashir said his country would only accept non-African troops from Pakistan or China.
A month ago the Jem attacked Sudan's Defra oilfield in the Kordofan region, run by a Chinese-controlled consortium, the Greater Nile Petroleum Operating Company.
Jem said at the time that the Chinese company had one week to leave Sudan.
An estimated 200,000 people have died during four-and-a-half years of fighting in Darfur, with a further two million people displaced.