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A second half strike from Ajax star Kudus Mohammed was cancelled by Percy Tau, as both teams shared the spoils.
The Black Stars are now mathematically guaranteed to finish in the top two of group C following the result against Bafana Bafana.
CK Akonnor’s side sits at the top of the group with 10 points – the same as South Africa – although the Black Stars have a better goal difference.
Ghana also has a better head-to-head record over both South Africa and Sudan, with the Falcons occupying third place with nine points.
Akonnor named a strong starting line-up that had a mixture of youth and experience due to the unavailability of some regular stars.
The absence of Andre Ayew, Jordan Ayew and Thomas Partey meant that midfielder Mubarak Wakaso was named stand-in captain against South Africa.
There were also debuts for Kwame Poku and Ismail Ganiyu, while Caleb Ekuban and Emmanuel Gyasi also got the nod in attack.
The Black Stars made a slow start to the game and were on the back foot for larger periods following a dominant display by Bafana Bafana.
The South Africans created some chances in the first half-hour, with Razak Abalora being called into action a couple of times.
Bafana Bafana’s two best chances of the first half fell to Morena, who fired into the side net on both occasions.
Ghana put up a better performance in the second half and Kudus deservedly opened the scoring just four minutes after the restart.
The lead was, however, short-lived as Tau equalised for South Africa three minutes later after firing a low shot past the onrushing Abalora.
Both teams created a couple of chances towards the end of the game but neither managed to snatch the winner as the game ended in a draw.
The result sees Ghana qualify for next year’s AFCON in Cameroon, although Bafana Bafana will have to get at least a draw against Sudan in their last group game to also seal qualification.