Thabo Senong's troops were aiming for a positive start to boost their hopes of qualifying for the U20 World Cup later this year.
South Africa started brightly as Keenan Abrahams went close to opening the scoring in the second minute while Nkosingiphile Ngcobo nearly caught Niger goalkeeper Khaled Ibrahim napping five minutes later with a lob that sailed just over the bar.
Despite Niger's dominance with the ball, more of the chances fell to the South Africans as Thabiso Monyane and Fezile Gcaba went close to breaking the deadlock in the final ten minutes of the first half.
The visitors eventually succumbed to pressure from the host nation in the 62nd minute as Boubacar Goumey found the breakthrough with a low shot at the far post.
Amajita managed to claw their way back into the clash and found the equaliser 20 minutes before time through substitute Siphesihle Mkhize with a stunning header inside the box.
The game swung from end to end in the last ten minutes as the sides pushed for the winner however, there was no dramatic ending as they shared the spoils in the opening clash in Group A.
Senong's side will now face Nigeria on Tuesday evening, with kick-off scheduled for 16h30.