Wakaso scored from a free-kick three minutes from time to hand the Black Stars the maximum points at the expense of the Amavubi, who put up an improved output cheered on by a partisan crowd at the Amahoro Stadium.
Elsewhere, Tanzania held visiting Nigeria to a barren draw in a Group G clash in Dar es Salaam.
In Windhoek, Senegal were too much for their hosts Namibia with a goal in each half from Cheikhou Kouyate and Sadio Mane deciding the Group K tie in their favour.
Burundi cruised to their first win of the campaign beating Niger 2-0 in Bujumbura. Fiston Abdul Razak scored the opener on 21 minutes before Fiston Papy sealed victory seven minutes from time.
In Group E, the Atlas Lions of Morocco made light of work their hosts Sao Tome & Principe in Sao Tome with a 3-0 win. Nordin Amrabat, Youssef El Arabi and Nabil Dirar scored in the first half was enough to ensure the North Africans maintained their 100 per cent record thus far.
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