Both sides looked to grow into the game, keeping the ball and building patiently from midfield.
Pirates looked to draw first blood, bursting forward through Luvuyo Memela, whose cross was deflected past Kyle Peters by Sifiso Hlanti in the 13th minute.
Bidvest Wits looked to bounce back immediately and tried to create chances down the flanks, Vincent Pule and Keegan Ritchie finding joy but failing to make the telling cross that would level matters.
The hosts were able to capitalise on a defensive error by Buhle Mkhwanazi, Mulenga intercepting a back pass and rounding Peters before slotting home at the front post.
The half got worse for Gavin Hunt’s men when Nazeer Allie was judged to have impeded Mulenga in the area, referee Hlungwani pointing to the spot.
Shonga converted his penalty-kick to give the hosts a commanding three goal lead as the sides went into the break.
The Clever Boys looked to influence the game through attacking substitutions and playing a higher press on Pirates.
Wits’ efforts to get back into the game saw them vulnerable on the counter, something that was exploited by Shonga after he picked up the ball in the midfield.
The Braamfontein outfit continued to push for a consolation goal. Majoro had a shot cleared off the line in the 82nd minute before winning a penalty two minutes later.
Siyabonga Mpontshane kept out Majoro’s effort from the spot and in doing so secured Pirates’ biggest victory of the season.