Thembinkosi Lorch started in the attack along with Bradley Grobler and Percy Tau up front, while Thato Mokeke, Dean Furman and Bongani Zungu made up the midfield.
Bafana were on the back foot right from the get go when Jordan Ayew threatened the goal on 10 minutes following a free-kick from Thomas Partey, but Bafana shot-stopper Ronwen Williams thwarted the attempt.
Grobler failed to put Bafana ahead four minutes later when he blazed over the top from close range following a goal-mouth scramble from an inviting delivery inside the area.
Bafana's bright start turned sour when Bongani Zungu limped off the pitch after 26 minutes following a knock and was replaced by Thapelo Morena two minutes later.
With 10 minutes left in the half, the Black Stars hit the front not long afterwards when Partey found the bottom corner with an effort from distance that left Williams stranded.
Bafana were slow off the mark in the second half as the Black Stars leaned towards a cushion from impressive but well drilled variations which had the visitors riddled with uncertainty. Within the 60th minute, Ghana left Bafana off the hook when Jordan Ayew curled inches wide after creating space from a tight angle whilst Partey lashed over the top from afar.
More firepower arrived from the South Africans three minutes later as Grobler went off for Lebogang Mothiba, whilst Kudus Mohammed replaced Alfred Duncan for the hosts.
The Ghanaians upped the tempo in the final 10 minutes when Thamsanqa Mkhize handded possession to Mohammed who found the top corner with a poweful strike from the edge of area.
Bafana failed to launch a comeback nor land a consolation soon afterwards, granting the Black Stars a comfortable victory and second place in the group.
Ghana: Ofori, Yiadom, Mensah, Aidoo, Nuhu, Baba, A. Ayew, Partey, Duncan, J.Ayew, Boateng.
Bafana: Williams, Mkhize, Hlatshwayo, Mkhwanazi, Hlanti, Furman, Zungu, Mokeke, Tau, Grobler, Lorch.
Subs: Keet, Mathoho, Morena, Maela, Lebusa, Phiri, Mvala, Manyama, Serero, Modiba, Mothiba, Erasmus.