Chippa got off to the best possible start, opening the scoring after just two minutes. Lehlonolo Nonyane gave away the corner. Thabo Rakhale whipped in a corner to the near post where Andile Mbenyane got the run on his marker and glanced the ball via a deflection in to the back of the net.
The hosts were growing in to the game more and more and were rewarded with the equalizer in the 20th minute and like Chippa's opener, it came from a corner. Deon Hotto delivered the set-piece to the back post with Nonyane heading it towards goal where Motupa was on hand to apply the finishing touch.
Seconds before half-time, the Clever Boys took the lead - once again from a set-piece. Hotto swung in a curling corner which was expertly headed in to the top right-hand corner by Dzvukamanja.
Wits started the second period as they finished the first - in the ascendancy. Motupa, as he is accustomed to doing, cut in off the left flank on to his favoured right foot and unleashed a powerful effort from outside the box which went narrowly wide of Mzimela's left-hand post in the 55th minute.
However, the Chilli Boys won a penalty in the 62nd minute after Mbenyane's cross hit the hand of Bafana left-back Sifiso Hlanti in the box. Boikanyo Komane converted from the spot with Keet guessing the right way and getting a touch to the ball but he could not prevent it from ultimately going in.
Wits deservedly restored their lead with ten minutes to go. Cole Alexander played Motupa in down the right-hand channel, who cut inside past his marker superbly before squaring the ball for Dzvukamanja to grab his brace with a neat finish.
After Hlanti fouled Manzini on the edge of the box, the visitors had a free-kick in a promising position. Up stepped substitute Ruzaigh Gamildien, who curled a beautiful strike in to the top left-hand corner and send the match in to extra time.
Chippa had the momentum now and capitalised by taking the lead in the fifth minute of extra time. Lerato Manzini got in behind the Wits defence down the right-hand side and squared the ball to the back post where replacement Rhulani Manzini was on hand to steer the ball past Keet from close range.
The Chilli Boys took their foot off the pedal and were punished when Kurt Lentjies gave the ball away sloppily to Pelembe. The Mozambican international delivered a beautiful cross to the back post where Hotto was on hand to volley the ball expertly in to the back of the net to send the match into a penalty shoot-out.
Mzimela, who didn't look very secure in goal in normal time, came to life in the penalty shoot-out, saving Wits' opening penalty from Pelembe - which would prove to be the crucial difference in the end as Chippa netted all their penalties with Rhulani Manzini scoring the winning spot-kick.
Wits: Keet, Mere, Mkhwanazi, Nonyane, Hlanti, Scott, Alexander, Motupa, Dzvukamanja, Hotto, Murray.
Subs: Goss, Weidlich, Ritchie, Monare, Majoro, Pelembe, Mhango.
Chippa: Mzimela, Macheke, Nsabiyumva, Shitolo, Tlolane, Malepe, Komane, Rakhale, Mayambela, Mbenyane. L.Manzini.
Subs: Mothwa, Lentjies, Makobela, R.Manzini, Klate, Gamildien, Malama.