The match, which was televised live, was played at Stade Seyin Kountche in Niamey.
The Flying Eagles dominated the match right from the blast of the whistle to the end of the match, but failed to register a goal, despite enjoying a 66% possession and 13 shots on goal, while South Africa had 34% possession and 4 shots on goal.
The efforts made by the Flying Eagles to beat their opponents, especially in the second half of the match, were frustrated by the South African goalkeeper, who struggled to maintain a clean sheet with his accurate saves.
With this score line, Nigeria lead Group A with 4 points, having defeated Burundi in their first match 2-0.
South Africa, which drew with Niger 1-1 in the opening match, are second with 2 points, while Niger are third with 1 point and Burundi are fourth with no points yet.
Niger will play Burundi later today for their second match in Group A.