Left-back Fawaaz Basadien struck as early as the second minute into the contest to put the home side into the lead.
Nkosikhona Radebe hit back to rescue a point for TS Galaxy with 18 minutes to go but that was not enough to stop the Rockets coach Sead Ramovic from resigning.
It was a missed opportunity by Stellenbosch to go third on the standings and stay in close check of leaders Orlando Pirates and second-placed Mamelodi Sundowns.
The Maroons remain fourth on the table with nine points fewer than the Buccaneers and six less than Sundowns while TS Galaxy remain rooted at the foot of the table in what forced Ramovic out of the club after three seasons.