Terrence Mashego, Tshegofatso Mabasa, and Vincent Pule were brought to the fore from Bafana's late win over Ghana, but Pule was hurt in the warm-up and Thabiso Kutumela took his place.
Hugo Broos' men were on top early on, and Siyanda Xulu came close to putting them ahead in the ninth minute with a thunderous header from a Teboho Mokoena cross that went just past the top corner.
Midway through the first half, Surafel Dagnachew came close to breaking the deadlock with a dipping effort from outside the area that goalkeeper Ronwen Williams tipped over the bar.
Broos was forced to make a substitution ten minutes before halftime when Mabasa went down with an injury and was replaced by Victor Letsoalo.
The Walia Ibex were creating chances in the final minutes of the first half, but Williams kept Bafana in the game with two one-on-one stops in the space of two minutes to deny Abubeker Nasser twice.
Bafana broke the stalemate at the near post on the stroke of halftime, when shot-stopper Fasil Gebremichael fumbled Mokoena's free-kick into his own net.
In the 67th minute, Getaneh Kebede equalized for Webetiu Abate's side with a stunning free-kick from the edge of the box that looped over the wall and into the top corner.
After pouncing on a deflected header from a long thrown in, Mothobi Mvala restored Bafana's lead four minutes later with a close-range shot inside the area.
In the final 12 minutes, Broos made a double substitution, with Evidence Makgopa replacing Kutumela up front and Yusuf Maart replacing Ethan Brooks in midfield, both for fresh legs.
Makgopa was unlucky not to make it 3-1 for South Africa with a looping header at the near post that bounced off the goal frame only minutes after coming on.
In stoppage time, Makgopa got his reward by lobbing Gebremichael during a counter-attack, and South Africa clinched first place in the group.
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