Sibusiso Vilakazi gave the Clever Boys an early lead with a side-footed finish from a Henrico Botes cutback from the right. Botes was played through by Elias Pelembe from midfield.
But Jeremy Brockie brought Matsatsantsa level in the 56th minute with the easiest of close-range headers from a pinpoint Dove Wome cross from the right to take the game into extra time.
Former SuperSport man Daine Klate came back to haunt the club after he netted with a glancing fiving header from Siyabonga Nhlapo's cross in the first half of extra time to give Wits a 2-1 lead.
Henrico Botes then put the result beyond doubt with a thunderous strike just a few minutes later. The Namibian targetman picked the ball up quite a far way from goal, turned his markers, who all back off, and the striker duly eccepted the invitaiton to rifle an unstoppable shot past Ronwen Williams.
The game also saw referee Victor Gomes dish out two reds cards – Buhle Mhkwanazi was sent off for a second yellow card in the 78th minute and Kingston Nkhatha talked his way into an early shower in stoppage time at the end of the second half.