Stanley Nwabali was the hero of the night as he saved two penalty kicks.
Nigeria were hoping to make it into their fourth AFCON final but were made to work for it early in the first half as South Africa bossed early proceedings.
Nigeria have come the first nation to reach the final of the 2023 African Cup of Nations in Ivory Coast after beating South Africa 4-2 on penalties after playing a 1-1 draw in 120 minutes on Wednesday.
Troost-Ekong fired Nigeria ahead on 54th minute after Victor Osimhen was fouled in the box and the Napoli forward thought he has killed off the game on 84th minute but VAR denied it before awarding South Africa a penalty which Mokoena scored on 87th minute.
Mundau missed a glorious chance on 94th minute after blasting over from a Mokoena’s free kick and after 30 minutes minutes of extra time, penalties followed.
Nigeria missed only one penalty kick while two South Africans failed to score. The Eagles will wait for the winner between Ivory Coast and DRC, who face in any minute now.
Last time Nigeria won the trophy was in 2013 in South Africa where they beat Burkina Faso 1-0 in the final to snatch it from Zambia.