Gavin Hunt’s men had the better chances on the night but had to twice come from a goal behind to level the score at 2-2, only to see a Lebogang Manyama-inspired City side snatch all three points with a 93rd minute winner.
The victory ensures City will stay top of the Absa Premiership standings for the entire weekend – they have a four point gap over SuperSport United who play Celtic on Sunday.
Although the Clever Boys enjoyed the early possession, it was the Cape side who took the lead after 11 minutes, Roland Putsche expertly firing in a low volley from 15-yards out after Aubrey Ngoma had dinked in a cross from the left wing.
It took Wits until the 22nd minute to create a decent chance at an equaliser, but Eleazar Rodgers was unable to get enough direction on his header from 10-yards out.
The Clever Boys continued to press for a goal and after Shu-aib Walters did brilliantly to deny new signing Siboniso Gaxa in the box, there was little the Cape shot-stopper could do to keep out Bongani Khumalo’s powerful header from a 31st minute corner.
The home side continued to look more threatening and could have taken the lead seven minutes before the break, but after climbing well in the box, Mogakolodi Ngele’s header went wide.
The Students started the second half in blistering style and had three chances in the first three minutes after the break to go in front.
But Elias Pelembe failed to get a decisive touch on Ngele’s tempting cross before Ngele had his snap-shot palmed onto the post by Walters and then Thabang Monareng fired into the stands from the edge of the box.
Their failure to convert good chances proved costly as City struck on 56 minutes, Manyama able to roll the ball into an empty net after Wits goalkeeper Darren Keet had made a complete hash of trying to cut out Putsche’s searching ball.
But the Students were to hit back within two minutes, Rodgers confidently converting from the spot after Walters had rushed off his line to try and prevent Ngele from reaching a long pass, but had succeeded only in tripping the Botswana international.
The closing 20 minutes of the game saw the hosts camped out in the Cape Town City half for the majority of the time.
But some excellent defending by Thamsanqa Mkhize stopped Gabadinho Mhango from pulling the trigger, while Cuthbert Malajila fired straight at Walters before Mhango again had a shot blocked.
City also had glimpses on goal before snatching victory deep in added time when Manyama headed in a back-post cross.
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