They beat hosts Benin 2-0 in a Group C match played at the Félix Houphouët Boigny Stadium in Abidjan on Tuesday night.
The win means they remain top of the group with 13 points from six matches, five points clear of Benin and Rwanda.
But South Africa could face the possibility of a points deduction from FIFA, following a crucial mistake made in the match against Lesotho on Friday.
Coach Hugo Broos fielded midfielder Tebogo Mokoena, despite the midfielder having received two yellow cards in previous qualifying matches.
Lesotho have lodged a complaint with CAF and FIFA, but after the 24-hour deadline and the verdict is not out yet.
--SABC--