The win sees Clever Boys move back to the top of the league standings, while the Buccaneers remain eighth on the table.
The visitors showed great intent in the early stages of the game and Wits goalkeeper Moeneeb Josephs was called into action just nine minutes into the game.
The experienced shot-stopper did well to deny Pirates midfielder Abbubaker Mobara, who had unleashed a snapshot which was saved by the former.
However, Wits were also attacking in numbers – with Phakamani Mahlambi looking to use his skill and pace to unlock the Pirates defence.
The speedy winger made a good run in the 26th minute, before playing a dangerous low cross which was cleared away by the Bucs defence.
It was end-to-end stuff and Josephs was called into action in the 40th minute when he gathered a Pirates midfielder Mpho Makola’s free-kick with ease.
Nevertheless, Wits and Pirates were locked at 0-0 during the halftime break, after an interesting first-half which saw neither side wanting to give anything away cheaply.
Pirates had a chance to score nine minutes after the restart, but Thamsanqa Gabuza could not convert Thabo Rakhale’s teasing cross into the Wits box.
But Bucs were left to rue that chance two minutes later when Mahlambi bursts into the box and substitute Cuthbert Malajila fired home a loose ball to make it 1-0 to Wits.
The visitors tried to respond with a goal in the 62nd minute – with Rakhale pulling the trigger from range, but Josephs was well-positioned to make a decent save.
Wits continued to attack after taking the lead and Frank Mhango forced Pirates goalkeeper Siyabonga Mpontshane into a good save eight minutes later.
With time running out, Bucs coach Kjell Jonevret introduced Dove Wome, who has netted three league goals for the Soweto giants, in the 77th minute.
However, Wits captain Thulani Hlatshwayo and his defence stood firm at the back in the remaining minutes and the home side ran out 1-0 winners.
Wits (0) 1 (Malajila 56′)
Pirates (0) 0
Wits: Josephs, Hlatshwayo, Khumalo, Frosler, Hlanti, Motshwari, Ntshangase, Monare, Myeni (Malajila 46′), Mahlambi (Pelembe 74′), Mhango (Pule 87′).
Pirates: Mpotshane, Gcaba (Ndoro 70′), Jele, Matlaba, Phungwayo, Sarr, Mobara, Manyisa, Rakhale (Wome 77′), Makola (Qalinge 70′), Gabuza.
Meanwhile Mamelodi Sundowns dropped two valuable points after they played to a 2-all draw against the struggling Platinum Stars in another league match also played last night at the Lucas Moripe Stadium.-www.psl.co.za