Wits pressed early on and Thomas Sweswe nearly scored when his low volley was saved by Tsepo Motsoeneng.
Ten minutes before the interval the visitors were unlucky not to score as they were denied by the woodwork. Wits keeper Ryan Harrison misjudged a 25-yard dipping shot by Anver Esterhuizen which came off the bar.
Three minutes after the break Wits forward Calvin Kadi nearly gave his side the lead from a bizarre situation when he spotted the keeper out of his area, but his shot from the halfway line went just wide.
In the 58th minute Wits took the lead when they were awarded a penalty with Kadi being brought down in the area. He stepped up and took the spot-kick himself.
The Clever Boys nearly doubled their lead in the 72nd minute when Matthew Pattison shaved the outside of the post with a low shot just from outside the box.
With four minutes remaining former Wits player Noah Chivuta nearly gave his side the equaliser, but his shot went just high.
But there would be heartbreak for the Clever Boys faithful when Stars got the equaliser with the last kick of the match.
Nomandela did really well to create space before beating Harrison as the small group of travelling Stars fans were sent into a frenzy.