Wakaso penalty sees Black Stars to victory.
Four-time champions Ghana defeated Mali 1-0 to go the top of Group B at the Africa Cup of Nations.
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The Black Stars have four points while Mali slipped to second place on three points.
Democratic Republic of Congo, who have collected one point, face pointless Niger later in the second game of a Nelson Mandela Bay Stadium double-header.
Ghana dominated this encounter with Mali lacking the firepower to trouble their opponents even after the introduction of fit-again West Ham striker Modibo Maiga.
Mubarak Wakaso put Ghana in front from the penalty spot in the 38th minute after the lively Emmanuel Agyeman Badu was brought down inside the box by experienced left-back Adama Tamboura.
Wakaso will miss his team’s final group game on Monday against Niger after he was booked for his celebration — his second caution of the competition.
Ghana coach Kwesi Appiah said: “We were much more tactically disciplined in this game than against DR Congo, but I know we can do a lot better than we did today.”
Captain Asamoah Gyan said: “It was a difficult game. We needed to win and now we have four points, but we need more to qualify to the next stage and so we will not underrate Niger.”
Mali coach Patrice Carteron said: “The referee did not help us because he ought to have sent off the Ghana goalkeeper rather than just booking him for handling the ball outside his area.
“Ghana were better, especially in the first half, but we still have a game to qualify for the next round and so we will forget this match and focus on our next game.”
This was the third time the west African countries clashed in the tournament within a year.
Ghana won a group game 2-0 in Gabon at the 2012 tournament before Mali gained revenge by winning 2-0 to clinch third place.
In a cautious first half, Ghana created more chances.
After eight minutes, Mali skipper Seydou Keita’s free kick from the top of the box, after goalkeeper Fatau Dauda handled outside his area, narrowly missed the target with the goalkeeper beaten.
Thereafter, it was Ghana all the way.
On 13 minutes, Gyan saw his shot from inside the box blocked for a corner.
Badu’s header in the 32nd minute off a Wakaso free-kick came back off the foot of the post with Mali goalkeeper Mamadou Samassa beaten.
Mali began the second half brightly and veteran Keita just failed to connect with a clever chip by Mahamane Traore, who had a shot tipped over by Dauda.
A Wakaso free-kick was not far off target and a Gyan shot nearly caught the Mali goalkeeper napping.
Badu had a free-kick scrambled away for a corner and substitute Solomon Asante almost made an immediate impact when he latched on to a loose ball only to miss.
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