The pre-tournament favourites have almost picked up their slot in the knockout stage, maintaining a clean sheet with a last group game in hand
Both goals came in the second half after the sides had battled it out in a tense but physical first half that saw few attempts on goal.
Al Ain marksman Gyan finally broke the deadlock in a tight game with a superb curling free kick that flew over the Malian wall and landed in the top left corner of goalkeeper Soumbeila Diakite’s goal.
The Eagles came close to equalising in the 67th minute through Modibo Maiga when he jumped above the Black Stars defence but his header shaved the top of goalkeeper Adam Kwarasey’s post to leave Ghana in the lead.
The climax of the second west African derby in Group D arrived in the 73rd minute when a back heel from Gyan set up Olympique Marseille’s Ayew, who brilliantly turned two of his markers inside out and curled a low shot into the corner of the goal to beat shot-stopper Diakite and double the lead of the four-time African champions.
Both teams started off with a great deal of respect to each other. It was a game characterised by tensed moments and physical challenges as both sides made few attempts on goal in the first half.
The first real chance surfaced when Ghana’s midfield creative force Kwadwo Asamoah unleashed a thunderbolt, which was parried by the Malian goalkeeper and Sulley Muntari’s rebound was off target.
The Udinese play-maker Asamoah was once again on hand for the Black Stars when he turned one of the Eagles’ defenders inside out, but his left-footed shot was off target.
It was a half full of fouls and close marking as the two west African countries looked determined to outdo each other.
With about seven minutes left before the interval, Cheick Tidiane Diabate took a breathtaking free kick that slammed off one post and onto the other despite Ghana shot-stopper Kwarasey spreading wide to cover the bottom right corner of his post. Abdou Traore was unlucky with his rebound under pressure, which was hit high above the intended target.
The two goals in the second half broke the silence at the Franceville Stadium in Gabon and arrived at the right time for the Black Stars.
The win gives Ghana a better chance of moving to the next stage of the continental showpiece, as they now top the group on six points, with Mali and Guinea on three and Botswana yet to register a positive result.