Bafana Bafana coached by Gordon Igesund needed only draw the game to make sure of their quarter-final place, and eliminate Nigeria coached by Stephen Keshi, in the process, but continue their poor string of results against the Super Eagles.
Attacker, Ejike Uzoenyi opened the scoring for Nigeria in the 22nd minute, when he connected Ifeanyi Ede's well laid pass from the left.
Ede made it 2-0 for Nigeria with a 32nd minute penalty after Gbolahan Salami was brought down by South Africa goalkeeper Moeneeb Josephs.
Ejike Uzoenyi completed his brace in the 64th minute to give Nigeria 3-0 lead after goalkeeper Chigozie Agbim, who had being calamitous in goal for the super eagles in the two previous matches denied South Africa a goal in the 61st minute,
Bernard Parker scored South Africa's consolation goal from the penalty spot in the 81st minutes after Ugonna Uzochukwu was adjudged to have brought down Matshego inside the 18-yard box.
Solomon Kwambe was red carded in the 74th for a second bookable offence, two minutes later South African's Vuyo Mere was sent off as well for a foul on Gbolahan Salami.
Captain and goalkeeper of the CHAN eagles, Chigozie Agbim had a great game ass he stopped the South African from getting a goal with world class save to put pundits and fans to shame for calling for his head especially after those two school boy error in the match aginst Mozambique.
The Eagles finished second in Group A with six points from three matches, behind Mali, who won their match against Mozambique by 2-1, with seven poin seven points.