Bafana Bafana captain Ronwen Williams was the key man again, as the quarter-final hero saved two spot-kicks.
First, DR Congo captain Chancel Mbemba had the chance to win it, only for Williams to block, before Meshack Elia’s penalty was also saved.
The game, which ended goalless, went straight to penalties after 90 minutes.
In the quarter-final win against Cape Verde, Williams saved four penalties in the shootout.
In Abidjan’s Felix Houphouet-Boigny stadium, he again proved key after Tebogo Mokoena, who has been a key factor in South Africa’s run in Ivory Coast, hit the post with the first penalty.
Shortly after the skipper secured South Africa’s success, Belgian coach Hugo Broos was given the bumps after adding a third-place finish to his 2017 triumph with Cameroon.
The last time South Africa finished on the podium was in 2000, when they defeated Tunisia on penalties, while DR Congo were looking for their best tournament since 1998.