Attacking midfielders Reeve Frosler and Nelson Maluleke were the heroes of the South Africans while Walid Attia Mourad got the consolation for the visitors.
The second leg will now take place in Egypt in two weeks time with the overall winners qualifying for the finals in Niger in March next year.
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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.