Andre Ayew's disputed first half penalty at Cape Coast was enough to allow Ghana to edge South Africa on goals scored after they both finished on 13 points in Group G, and with the same goal difference.
The Democratic Republic of Congo also won their World Cup qualifying group on Sunday. DR Congo beat Benin 2-0 in Kinshasa to finish one point ahead of their visitors in Group J. DR Congo were awarded a generous penalty inside the opening 10 minutes to allow veteran striker Dieumerci Mbokani to give his side the lead. Ben Malongo added the second with a close-range header with some 15 minutes left.
The Congolese finished with 11 points, one more than Benin.
The 10 group winners play five two-legged ties to decide the African representation for Qatar and the remaining four group winners will be decided on Tuesday.
Also on Sunday, Ismaila Sarr scored a double for Senegal as they beat Congo 2-0 in Dakar to finish their group campaign unbeaten. They also amassed 16 points in Group H but had already booked their place last month.