Wits looked lively from the start, but lacked sharpness in front of goal. Polokwane looked to play most of their football on the counter, trying to catch The Clever Boys on the break.
The hosts created a flurry of chances in the opening exchanges with Mxolisi Macuphu and Deon Hotto looking threatening.
City were reduced to 10 men at the 20 minute mark after a nasty challenge on Thabang Monare by Salulani Phiri.
George Chigova was outstanding for the visitors in the opening half, arguably his best moment coming in the 40th minute to deny Macuphu who had been played in by Gift Motupa. The shot-stopper denying the Wits striker from point-blank range.
The game then became fragmented and scrappy towards half time, the sides heading into the break locked at 0-0 with neither finding the all important opener.
An injury forced substitution saw Vuyo Mere replace Buhle Mkhwanazi at the start of the second half, the latter struggling with a muscle strain in his back.
The visitors looked to galvanise their troops after going a man down and came out swinging in the second half, looking to expose Gavin Hunt’s men.
With a quarter of an hour left to play, veteran Jabulani Maluleke put the visitors ahead from a well struck free kick.
The Clever Boys looked for an immediate response through Sifiso Hlanti, but the effort was unable to beat Chigova.
The City keeper was the difference in the closing seconds as he denied Terrence Dzvukamanja from close range.