Defenders Siyabonga Sangweni and Thabo Matlaba were the goal heroes, scoring after the break following the dullest of opening halves.
Thulani Hlatshwayo and Daine Klate had shots sail over the bar before Sangweni missed the first 45 minutes’ best chance, heading wide from a corner-kick.
However, he did not make the same mistake on 55 minutes, volleying home Daine Klate’s corner after the Wits defenders fluffed their lines.
Toriq Losper looked to have equalised soon after when he connected with Sibusiso Vilakazi’s cross, but Senzo Meyiwa was at his best to deny the former Ajax Cape Town man from close range.
Pirates then further strengthened their position in the 73rd minute when Matlaba showed blistering pace to outsprint the defence and slot under the body of Jackson Mabokgwane.
The Buccaneers had a few more half-chances towards the end of the match as Wits pushed forward, but the match finished 2-0, handing Vladimir Vermezovic’s team the advantage leading into the second leg next week.