Fisayo Dele-Bashiru scored the first goal for the Finidi George era as the Super Eagles came from a goal down to record a third straight 1-1 in the 2026 FIFA World Cup qualifiers.
Themba Zwane put South Africa ahead with a sumptuous finish leaving the Nigerian defence dead for the first goal in the 29th minute.
The Nigerian team struggled in the first half, leaving spaces behind for the South Africans to explore and they almost got more goals.
The first half ended with Nigeria behind, but all that changed with an early second-half goal in the 46th minute from Fisayo Dele-Bashiru.
Fisayo received a pass and made a quick turn at the edge of the South African box before unleashing a shot to level matters.
The goal finally brought the Eagles into the game, with both sides having a go at each other in an open game.
Two quick chances on both sides almost changed the result with Percy Tau skewing a shot, when alone with Nwabali at his mercy while Chukwueze hit the bar minutes later.
In added minutes, the two goalkeepers were called into action.
Rowen Williams dived low to save a goal-bound shot from Lookman before Nwabali ran out of goal to kill off a dangerous move from South Africa.
The result keeps Nigeria fifth with three points on the table as Lesotho keep their lead from a 2-0 win earlier in the day.
South Africa is in fourth position ahead of Nigeria with one point.