Sunday's result was Stellenbosch's third consecutive victory in Group B after starting the campaign with two straight defeats.
In a show of character, they managed to pick themselves up and they have now qualified for the Last-eight with a match to spare.
They now have four points fewer than log leaders RS Berkane who were held 0-0 by Desportivo Lunda-Sul away in Angola.
Ahead of the final day of this group stage, Stellenbosch are now an unassailable five points clear of third-placed Stade Malien.
Steve Barker's men can even afford to lose their last game against RS Berkane.