Steve Komphela’s side produced yet another lackluster display, with Ghana by far the better team on the day.
Asamoah Gyan handed the Meteors the lead in the 13th minute with a striker from close range following a superb build-up.
The hosts completely dominated proceedings and doubled their lead in the 35th minute when Bernard Kumordzi headed home.
The score remained 2-0 at half-time.
The visitors started the second half in better fashion and pulled one back in the 56th minute when Eleazor Rodgers headed home from a cross by Bryce Moon.
Ghana’s Daniel Addo almost handed the South Africans an equaliser in the 69th minute, but his attempted clearance struck the upright.
However, Gyan put the result beyond doubt when he scored five minutes from the end to end the visitors’ dream of playing in next year’s Olympics.