Captain Andrew Ayew - in his 100th appearance - scored from the penalty spot in the 33rd minute as the Black Stars advanced to the World Cup qualifying playoffs as winners of Group G.
Ayew's strike proved decisive as Ghana finished as group winners thanks to a tie-breaker of a superior number of goals scored with both teams on 13 points.
The group decider was shrouded in controversy after Ghana were awarded a dubious penalty as Bafana defender Rushine de Reuck was adjudged to have committed a foul in the area from a corner kick.
Bafana Bafana head coach Hugo Broos after the final whistle hit out at the officiating and referee Ndiaye Maguette.
"I am very disappointed in the result but I'm proud of my players. But I have to say, the referee today allowed Ghana to be too aggressive.
"I have nothing against aggressive play but it has to be legal aggression."
Former players and coaches such as Pienaar and Mosimane, alongside many others, blasted Maguette's controversial penalty decision.
"How was that a penalty? Disgrace @CAF_Online," Pienaar tweeted to his over 380 000 Twitter followers.
— Usher Komugisha (@UsherKomugisha) November 14, 2021