Ghana led in the 49th minute by Mohamed Quddous, the Ajax Amsterdam playmaker, who returned to score the net against South Africa after scoring in the first leg.
But South Africa quickly equalized in the 51st minute through Brighton player Percy Tao.
Tao scored his 13th international goal in the Bafana Bafana jersey, and scored his fourth goal in the last 3 matches in the African qualifiers.
To raise the Ghana national team to 10 points in the lead, difference between direct confrontations from South Africa, which also raised its tally to 10 points in second place.
Sudan is third with nine points, and Sao Tome and Principe is in fourth – last – without any points.
The match saw Pyramids striker John Antwi remaining on the Ghanaian bench without participating.
Chances to qualify
The final round a few days later will be decisive in determining the identity of the second finalist from the fiery third group.
The date will be March 28, and South Africa will be hosted by Sudan, Omdurman. While Ghana will host Sao Tome and Principe in a ranking match.
Ghana needs to win to secure the top of the group, and a draw is sufficient if South Africa does not win against Sudan.
While the winner from Sudan and South Africa qualifies for the finals, and a draw will be sufficient for South Africa to qualify without entering into accounts.
While Sudan needs to win only and nothing else, because the tie will automatically rise to Ghana and South Africa.
Draws between Sudan and Ghana on points will benefit Ghana, who are better off in direct confrontations 2-1 against Sudan, which has already decided Ghanas qualification.