The pressing game deployed by the Nigerian side effectively in the first half somewhat cooled in the second half albeit Nazifu Mohammed's long range strike in the 78th minute almost broke the deadlock.
Nigeria's Paschal Durugbor pounced on a poor clearance by the South African keeper Kubehka but his rasping shot from a lovely swivel missed target.
The impressive South African keeper also saved a powerful shot from 25 yards from Muhammad Muhammad with five minutes left to play.
The Eagles will need a draw or outright win depending to confirm qualification for the semi-finals and ultimately the FIFA U-20 World Cup in Poland.
In the other Group A tie, hosts Niger defeated Burundi 3-1 to make brighter their chances of advancing to the semi-final stage, and securing a ticket to the FIFA U-20 World Cup in Poland.