Nigeria were stunned by South Africa’s two second half goals at the Godswill Akpabio International Stadium in Uyo.
The Super Eagles of Nigeria were very confident ahead of the game with the record of never losing a competitive game to the South Africa.
Eagles boss Gernot Rohr stuck with most of the starting XI he used for in the 3-0 win over Togo in a friendly game a week ago.
Ahmed Musa was a surprise omission as Moses Simon started in a front three with Kelechi Iheanaco and Alex Iwobi.
In midfield, captain of the day Ogenyi Onazi started alongside Wilfred Ndidi and Oghenekaro Etebo while the back four of Abdullahi Shehu, Chidozie Awaziem, William Troost-Ekong and Elderson Echiejile were infront of goalkeeper Daniel Akpeyi.
Super Eagles started brightly but Bafana Bafana gradually got into the game and got the best chance of the first half in the 41st minute.
The South Africans should have taken the lead but hit the post after Akpeyi spilled a cross.
It was all South Africa in the second half as Bafana Bafana controlled the game.
They took the lead in the 55th minute through Tokelo Rantie whose great header from a Ramahlwe Mphahlele beat Akpeyi.
With the Super Eagles searching for an equaliser, the Bafana Bafana sealed the win with a goal from counter attack.
Keagan Dolly quickly released Percy Tau who had only the Super Eagles goalkeeper to beat before slotting home.