The victory saw Shakes Mashaba breathe a sigh of relief after his side failed to book their place in the 2017 Afcon.
A solitary goal in an otherwise dour affair, gave Bafana somewhat of a consolation victory over the Pharoahs.
A rush of blood to the brain for South Africa saw them string together some neat passes that resulted in Mpho Makola heading Mandla Masango's cross in comfortably.
There was little else to speak of thereafter as both teams struggled in the final third.
The 2018 World Cup qualifiers are next for Mashaba and his troops, which get underway next month.
