Khubeka proved his worth with a number of fine stops.
Senong's side created little in the opening stages, with Nkosingiphile Ngcobo and Keenan Phillips seeing half-chances snuffed out by the alert Nigerian defence.
At the other end, Nazifi Yahaya shot into the side-netting in what was the best chance of the half for the Flying Eagles.
Nigeria dominated the possession in the second half but heroic SA defending and good organisation of his backline by Khubeka kept them at bay.
Amajita were looking to hit the west Africans on the counter-attack, but too often they could not find the right pass on a hard, bumpy surface that made moving the ball accurately on the pitch a challenge.
When SA did get the ball in advanced positions on the pitch, they lacked the numbers in attack to pick apart their opponents.
Nigeria continued to pepper the Amajita goal with shots from distance in the closing stages, but their aim was wayward, bar one smart low save for Khubeka from Muhammad Jamil in the closing minutes.