Algeria were a threat with powerful shots and it paid off when Abdennour Belhicini struck from outside the box to give Bafana Bafana goalkeeper Samukelo Xulu no chance and hand the Desert Foxes a 29th-minute lead.
But Molefi Ntseki's side hit back on the stroke of halftime when Thabiso Kutumela finished a Menzi Msuku feed.
The North Africans had better chances in the second half with Aimen Mahious coming close twice, but failed to utilise the opportunities as South Africa held on and managed to avert danger.
A scary moment for Bafana was witnessed deep in stoppage time when Medhi Merghem appeared to have been fouled by Thamsanqa Masiya to leave the Algerians protesting for a penalty which the referee denied to hand them.
After gaining a point from this 1-1 draw, South Africa would be keen to build on that going forward as Algeria maintain Group C lead with four points from two games