Wits dominated the majority of the game, but missed chances in front of goal proved costly as Pirates snatched a late win after they were denied a penalty in extra-time.
There were fears that another Bucs player was to be added to the long injury list when Mpho Makola suffered a heavy knock in the opening minutes of the game.
After receiving some medical attention Makola seemed fine to continue, much to relief of coach Roger De Sa.
Wits were playing some great football through the likes of Ryan Chapman, Mazikayise Mashaba and Bryce Moon, yet they still failed to break the deadlock by mid-way through the first-half.
Meyiwa got a finger to Papy Faty’s shot from outside the box to deny Wits from scoring.
Bryce Moon then wasted the perfect opportunity to put his side ahead just before the break, when he flashed his effort wide at the near post, following some fantastic one-touch passing across the face of goal by Wits.
Wits got the second half going by playing attacking football like they did in the first-half.
Even with all their possession and chances in front of goal, Wits poor in their finishing, but credit must also be given to Meyiwa, who pulled off several great saves.
In the 77th minute Makola wasted a chance in front of goal by hammering the ball straight at Baron.
Bucs were wrongly denied a penalty in the final stages of the game, after Ndumiso Mabela was brought down in the box.
Baron was injured in that challenge, with what looked like a broken leg, and he was replaced by Jethrin Barr, who was making his debut.
Pirates got their own back, however, as Sifiso Myeni came on and struck a ball into the back of the net following some scrappy defending to give his side the 1-0 win.