Thabo Senong named a number of Absa Premiership-based players in the line-up, with Lyle Foster, Wiseman Meyiwa and Kobamelo Kodisang being handed starts.
The South Africans failed to carve out any serious openings in the first half, which saw them enter the halftime break level at 0-0.
However, Senong's men broke the deadlock in the 61st minute thanks to a strike from Tashreeq Matthews.
However, Mozambique found the equaliser with eight minutes remaining, with Kamo-Kamo Cumbane firing past Khulekani Kubheka.
Amajita did have a couple more chances in the closing stages, but Mozambique held on for the draw.