Usuthu had led through Nkosinathi Mthiyane’s second half goal, but the substitute ensured the Students kept their unbeaten start to the season going, despite the late sending off of Koffi Dan Kowa for a second yellow.
Wits started the better of the two sides, and Musa Bilankulu should have done better in the 17th minute when he headed over from close range from Bongolwethu Jayiya’s free-kick.
Sthembiso Ngcobo, starting ahead of the in-form Bongani Ndulula, should have done better four minutes later when he turned well in the box, but fired wide with Moeneeb Josephs wrong-footed.
Benjani Mwaruwari should have given his side a half-time lead when he found himself one-on-one with Tapuwa Kapini, but he fluffed his lines.
Despite the loss of skipper Marc van Heerden to injury, Usuthu took the lead on the hour-mark. Former Thanda Royal Zulu man Mthiyane made no mistake after being set up by Ayanda Dlamini, though the defence should take some blame for completely switching off.
With the match heading for a draw, Kapini committed the mother of all blunders.
Trying to play for time, his antics backfired as he lost the ball under his body and, with only with an open net facing him, Kedebe tapped in injury-time to break Usuthu hearts.