Jamie Webber bagged a 79th minute equaliser for South Africa after a 68th minute opener from Mohamed Hassan.
Former Bafana and Kaizer Chiefs coach Molefi Ntseki took charge of the side for this tie and saw his mixed bag of fringe club players struggle to find any form of rhythm in the first half.
Monnapule Saleng came close from an early corner with a shot that he basted over the poles, ahead of a curled Neo Maema shot that was plucked out of the air by Pharaohs goalkeeper Mahmoud Abou El Saoud.
Saleng was Bafana's liveliest player after the break as well and beat Mohamed Gaber to create space for a 58th minute chance, but El Saoud made a good low save.
Ntseki's side inability to find a goal came back to haunt them as Hassan volleyed home a superb shot past goalkeeper Samukelo Xulu.
But Webber popped up with a similarly powerful effort minutes later to beat El Saoud and give his side a chance ahead of the second leg on Sunday.
Bafana Bafana forward Percy Tau has responded to growing criticism over his recent performances and absence from the national team, insisting he still has a significant role to play in South Africa's football plans.
Kaizer Chiefs' Thabo Cele admits he is desperate to overcome his recent injuries and turn out for Bafana Bafana.
Bafana Bafana suffered a 3-0 defeat to Angola in the final of the COSAFA Cup at the Free State Stadium on Sunday.
South Africa's Bafana Bafana stormed into the COSAFA Cup final with a commanding 3-1 victory over Comoros in the semi-final at Free State Stadium on Friday evening.
