Attacking midfielders Reeve Frosler and Nelson Maluleke were the heroes for the South Africans while Walid Attia Mourad got the consolation goal for the visitors.
The second leg will take place in Egypt in two weeks' time with the overall winners qualifying for the finals in Niger in March next year.
“I will take the 2-1 win although with a bit of good fortune we could have scored a couple more goals. We will take the fight to the Egyptians in the second leg and if we can score early, we will be in total control of our destiny,” said Amajimbos mentor Molefi Ntseki.
The home team dominated in the early stages and their early lead was a true reflection of the game. Although the visitors equalised late in the first half, South Africa again took the lead early in the second half and were never going to relinquish the lead.
