Benin are seeking to qualify for the 2010 Africa Cup of Nations
Mali and Benin secured their places at next year's African Cup of Nations in Angola after sealing home wins on Sunday.
Ghana recorded their first defeat in the second phase of the 2010 World Cup qualifiers after they were beaten 1-0 in Benin.
Frederic Kanoute scored in the 89th minute for Mali to beat 10-man Sudan 1-0 in Bamako in the Group D game.
Mali are second with eight points in the group, four behind Ghana while Benin are third with seven points
They cannot be overtaken by Sudan who have just one point with only a game remaining in the group.
Mohammed Aoudou's injury time goal in Cotonou ensured that the Black Stars conceded their first goal in the qualifiers.
Ghana, who sealed their World Cup spot last month, were hoping to maintain their 100 per cent record in the qualifiers but they met a determined Benin side.
The home side, led in attack by striker Razak Omotoyossi, dominated the game but they met goalkeeper Richard Kingston in good form for the Black Stars.
But the Wigan shot-stopper's stubborn resistance was broken in injury time when Aoudou arrived unchallenged to volley home.
Meanwhile, Sudan played with ten men in their game in Mali as defender Saeed Mustapha Balla was sent off in the 41st minute.
But despite playing with three strikers, Mali failed to break down Sudan's stubborn defence until Kanoute struck late in the Group D match.
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