The visitors started well, with the first real chance of the encounter falling to Thulani Hlatshwayo. His shot with the outside of his boot swerved toward goal but went just wide of the mark.
Chiefs grew into the game and found their first real chance when Ramahlwe Mphahlele picked out Leonardo Castro but the striker failed to guide his effort on target.
The visitors found the breakthrough in the 23rd minute through Deon Hotto. The Namibian bagged his second goal in as many games with a screamer from outside the area.
The equaliser came less than 10 minutes later for the hosts, with Castro heading home a free kick from Khama Billiat in the 32nd minute.
The leveller was all that was needed to reignite The Clever Boys, who went ahead in the 43rd minute through Terrence Dzvukamanja who headed home a wonderful cross from Sifiso Hlanti.
The sides went into the break with Wits buoyed by their first half display.
The second half saw things turn from bad to worse for Chiefs. Gift Motupa was on hand to slot home cooly after a through ball by Hotto found him one-on-one with Khune.
The win sees Bidvest Wits stay top of the Absa Premiership log with six points from their first two encounters while Kaizer Chiefs are in 10th spot with one point from a possible six for them.
Bidvest wits take on Orlando Pirates on Wednesday, 15 August 2018 at the Orlando Stadium. Kick off is set for 19H30