Nigeria began their campaign with a 2-0 win over Burundi, while Amajita drew 1-1 with the hosts in their opener over the weekend.
The Nigerians saw a lot of the ball in the early stages, but it was South Africa who had the first opening when Siphesihle Mkhize was denied by Kopano Thuntsane.
Other than the Mkhize opening, Amajita were unable to mount any serious openings at goal as they struggled to get out of their own half for most of the stanza.
Thabo Senong wasted no time in making a change for the second half as the pacy Promise Mkhuma came on for debutant Luvuyo Phewa.
However, the second half did not pan out any different from the first as both nations were unable to mount any serious attempts at goal.
Nigeria had to wait until the final stages of the half to carve out chances, but Amajita goalkeeper Khulekani Kubheka produced a couple key saves to ensure South Africa walked way with a point.
South Africa will now shift focus to Friday's final Group A encounter with Burundi.