Ghana, who drew the first leg 0-0 in Mitsamiouli last Friday, struggled to break down minnows Comoros and had to wait until the final five minutes to make the tie safe thanks to a second goal from Aston Villa forward Jordan Ayew.
Comoros finished the game with 10 men after Omar Mdahoma was sent off with 15 minutes remaining.
Wakaso’s moment of brilliance separated the sides at halftime. He bent his left-footed free kick over the wall and into the corner of the net on 18 minutes.
Comoros had a number of opportunities to draw level before Ayew lifted the tension in Kumasi.
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Twenty countries will emerge from the knockout ties to play in the group phase, which starts late next year.
(Reporting by Nick Said; editing by Toby Davis)
