But it was hardly an inspired performance from Shakes Mashaba's side, who looked good in the opening 20 minutes but then faded badly as the game wore on, leaving Egyptian goalkeeper Ahmed El-Shenawy a virtugal spectator.
With plenty of talk that this could be the last game in charge for Bafana Bafana coach Shakes Mashaba, he got the win he desperately needed, but the performance could still coun against him.
Mashaba persisted with lone striker Thamsanqa Gabuza, but was been able to recall Keagan Dolly after the Mamelodi Sundowns man missed the 1-1 draw with Mauritania with a hamstring injury.
Starts for Dean Furman and Mandla Masango were the other changes from the side that played in Mbombela.
After Koka had gone close for Egypt, Bafana had the lead when Mandla Masango's inch-perfect cross was superbly headed home by Makola.
Makola then had a chance to double the advantage when neat play from Dolly saw him find space in the box, but the Orlando Pirates man chose to shoot from an angle rather than cross and El-Shenawy made the save in the Egyptian goal.
It remained 0-0 at the break with few additional chances, but the visitors had a great chance to equalise minutes into the second period, but Ibrahim Salah put his header well wide.
Mohamed Salah then foudn space on the edge of the box, but his side-footed effort went just wide with Khune stranded.
Masango led a fast counter-attack for the home side, but having made space for the shot, was disappointingly off-target.
That was the last of the openings in a dire second period with Mashaba using his substitutes bench to close out the game.
South Africa: Khune, Mobara (Mphahlele 61'), Daniels, Hlatshwayo, Langerman (Hlanti 81'), Jali, Furman, Makola, Masango (Mekoa 77'), Dolly (Kekana 66'), Gabuza (Vilakazi 61').
Egypt: Shenawy, Gaber (Fathy 76'), Gabr, Dweidar, Abdel Shafy, Elneny (Hamed 63'), I.Salah, El Said (Sobhy 78'), Trézéguet, M.Salah, Koka (Gamal 80').