This was Stellies second win of the season, with Pirates suffering their third loss of the season.
The win for Stellenbosch at home takes them to position nine on the log.
The two teams met in the last-16 of the Telkom Knockout a week ago, with Stellenbosch offering a lot of resistance in Orlando – but Pirates ultimately won the match with a late solitary goal.
Stellenbosch made several changes to the team that started in the last match, with Pirates captain Happy Jele missing in central defence due to suspension.
A defensive blunder by Alfred Ndengane allowed Iqraam Ryners to punish the visitors in the 21st minute.
Pirates keeper Wayne Sandilands had to make a double save three minutes later to keep his side in the game. Despite dominating ball possession in the first half Bucs were trailing 1-0l at the break.
The visitors made a double substitution in the beginning of the second half, with Kabelo Dlamini and Gabadinho Mhlango given a run. Bucs kept on probing and Stellies keeper Boy de Jong made two brilliant saves within a space of a minute. Pirates’ penalty appeal was turned down in the 68th minute.
Sandilands was nearly caught off his line after a long range shot by Marc van Heerden.
Substitute Justin Shonga’s header went narrowly wide eleven minutes from time.
Pirates camped in the opposition’s half in the dying minutes but failed to get the much needed equaliser. Tshegofatso Mabasa was denied by the post after a brilliant overhead kick on the stroke of full time.
In another match Golden Arrows beat Polokwane City 2-1 to move to fifth spot on the log.