The opening exchanges saw the sides looking to establish their rhythm, with most of the action taking place in hotly contested midfield battles.
The first real chance of the encounter fell to Justin Shonga who drew a great save out of Darren Keet to keep the sides level.
The visitors were keen to ensure that they created plenty chances of their own. Deon Hotto found Siyabonga Mpontshane who made a save to deny the striker.
Gift Motupa looked to hand The Clever Boys the lead with a neat flick and shot but his effort rocketed over the bar.
Pirates found themselves in a good area through Augustine Mulenga, but Wits did well to crowd him out and ensure his shot was blocked in the 32nd minute.
A errant pass by Wits fell to Shonga’s feet and the Zambian found himself one-on-one with Keet and again the keeper was able to deny the striker.
The sides went into the break locked at 0-0 but it was clear that both sides were pushing for a result.
Pirates came close to opening the scoring through former Clever Boy, Vincent Pule, when he struck the upright with a shot from range.
Newly introduced substitute Haashim Domingo helped Wits grab a late lead. A strong run into the box allowed him to drive a pass across the face of goal which deflected in off of Gladwin Shitolo in the 80th minute.
The result sees Bidvest Wits move three points clear at the top of the Absa Premiership log for the time being with Pirates in 6th with four points from three games.