Amakhosi have been in fine form in the league of late and took the lead at the FNB Stadium through Flavio Silva after 35 minutes.
But Stellies were back on level terms when Langelihle Phili equalised five minutes into the second half, and Devin Titus completed the comeback with the winning goal after 86 minutes of the match.
The result left Chiefs in fourth place on the league standings with 30 points from 16 games, two adrift of Sekhukhune United in third, but with two games in hand.
Speaking after the game, Ben Youssef said he was sorry for the result while admitting that Stellenbosch were the better team on the night.
"First we have to apologise to our fans. We are so sorry for this result," he said in the Sowetan.
"I think we dominated the first half — we were better than Stellenbosch as we created a lot of scoring opportunities."
Ben Youssef added that his team were guilty of a number of missed chances, which doesn't bode well for the upcoming Soweto derby with rivals Orlando Pirates at the weekend, and comes on the back of two CAF Confederation Cup losses and their elimination from the Nedbank Cup - at the hands of Stellenbosch.
"We missed a lot of chances in the first half. I said it before and I am repeating it again: when you are better than the opponent, you have to finish off your chances," he said.
“We started the second half badly, conceding the first goal in the first five minutes. Then we tried to make a substitution, who we thought would add value — but I think Stellenbosch were better and they deserve to win this game.”