Fredi Kanoute scored twice but could not lead Mali to a win
Sudan have secured their first points on the road to Angola and South Africa in 2010.
Hosting the Group 10 leaders Mali, they posted a 3-2 win to make it three points from two games.
Their first match, which had been scheduled against Chad, did not take place because of political concerns.
Amir Damar Kuku put the home side in front in Khartoum on the stroke of half-time, before Mali's Fredi Kanoute equalised.
Kanoute scored again in the last minute of the game but by that time Sudan had secured the win with two more goals.
Earlier Chad secured their first win on the road to the World Cup in South Africa.
They beat Congo-Brazzaville 2-1 in N'Djamena to put their first points on the board in this campaign.
The visitors took the lead on 30 minutes, but two goals early in the second half gave Chad the win.
They can still qualify for the World Cup in 2010, but have been thrown out of the Nations Cup by CAF because of their failure to arrive for their match against Sudan.
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