A penalty by Marumo Gallants sank Cape Town City 1-0 at Dr Petrus Molemela Stadium on Saturday.
Edgar Manaka struck from the penalty spot after 12 minutes after Gabadinho Mhango had been brought down inside the box.
The result saw City's two-match winning run of beating Kaizer Chiefs and Orlando Pirates come to a halt and they remain sixth on the table as they failed to get into the top-four.
Gallants remained 13th in the standings, but they are now three points behind seventh-placed Cape Town City.