Cape Town - Defending champions Wits paid the price for their wastefulness as Golden Arrows claimed a 3-1 win at the Bidvest Stadium on Wednesday.
The Students made the better start and created two early chances for new signing Amr Gamal, who tested Nkosingiphile Gumede in the fifth minute before heading over a cross from Daylon Claasen two minutes later.
Reeve Frosler fashioned space for himself in the 19th minute with a sharp turn to lose his marker and get off a shot that was saved by Gumede, who also denied Gamal on the volley soon afterwards following good control by the Egyptian on his chest.
However, Abafana Bes'thende would break the deadlock with their first opportunity on 32 minutes when Lerato Lamola converted a low cross at the back post.
The hosts looked to respond and Frank Mhango thought he was in on 36 minutes, but Gumede pulled off a smart save to deny the striker.
They were back on level terms just moments later, though, and Gamal would not be denied as he pooped up at the back post to slot home a low cross.
There were no further chance before half-time, but Mhango threatened just five minutes into the second half as he skinned his marker before seeing his shot blocked.
Arrows then restored their lead on the counter in the 55th minute as Zolani Nkombela scored with only their second attempt on the night to stun the champs.
Claasen nearly hit back instantly for Wits with a shot that he dragged wide of the post two minutes later, while Gamal squandered another chance when he volleyed high over the goal from Nazeer Allie's cross on 72 minutes.
Eleazar Rodgers directed a free header straight at Gumede in the 78th minute and Gamal failed to hit the target once more 10 minutes later with an acrobatic effort from close range.
With the Clever Boys pushing for a late equaliser, they were hit on the counter as Kudakwashe Mahachi played in Nduduzo Sibiya to seal a 3-1 win in the final minute.