A compromise was reached that Sudan would take over this year in the hope that the conflict in Darfur, which has killed an estimated 200,000 people and driven 2.5 million from their homes, would have ended.
However, human rights groups and Western governments said there had been no improvement since last year and that Sudan should be barred from leading the organisation.
Delegates at the summit said a deal was agreed through the mediation of the South African president, Thabo Mbeki, and a group of seven respected presidents or "wise men".
|Thousands have been displaced by the|
conflict in Darfur. [EPA]
Al Jazeera's Haru Muntasa says delegates are generally happy with the outcome.
"The Sudanese delegation are saying that they have been willing to compromise for the sake of African unity."
In his opening speech, Konare accused Khartoum of attacking civilians in Darfur, where the United States says genocide has occurred.
"We appeal to the government of Sudan to stop attacking and bombarding Darfur and instead restore peace," he said.
The Sudanese government is accused of supporting Janjawid militias blamed for some of the worst atrocities of the conflict.
The US has described the killings as genocide.
Khartoum has repeatedly blocked the deployment of UN peacekeepers to support an overstretched African Union peacekeeping mission of 7,000 soldiers and monitors.
Chad, whose relations with Sudan are severely strained after the Darfur conflict spilled over their border, had vowed to withdraw from the AU if Sudan assumed the leadership.
And at the weekend, rebel groups in Darfur threatened to attack AU peacekeepers if Sudan assumed the presidency of the body.