January signing Glody Lilepo headed in a cross by Gaston Sirino to hand Kaizer Chiefs the lead four minutes into the match in a match played at Athlone Stadium.
The result saw Chiefs completing a league double over Stellenbosch whom they beat 2-1 in the reverse fixture in January.
The Soweto giants are now fourth on the log after Lilepo scored for the first time for Amakhosi.