The home side signalled their intent early on and they took the lead in the 20th minute through Gerald Phiri's fine finish from eight-yards out.
Pirates nearly pulled themselves level a few minutes later when Thabo Qalinge rattled the frame of the goal from 12-yards out.
Wits were on the front for most of the opening 20 minutes with Amr Gamal and James Keene proving tough to handle for the visitors' defence.
The Clever Boys went agonisingly close to doubling their lead on 35 minutes when Reeve Frosler's long range effort went narrowly wide of Wayne Sandilands' goal.
The half ended on a hour sour note for Wits as Phumlani Ntshangase had to be stretchered off after a challenge from Thamsanqa Gabuz however he did return to the pitch.
Pirates opted for a change shortly after the break, as Lyle Foster made way for Thabiso Kutumela.
The Buccaneers had most of the position in the first half, but were finding it tough to carve out chances, which prompted Milutin Sredojevic to introduced Mpho Makola and Bernard Morrison.
Moneeb Josephs came to Wits' rescue in the 69th minute as he produced a fine save to deny Mpho Makola.
Pirates pushed numbers forward and were camped in the Wits for the final 15 minutes of the half.
However, the Clever Boys defence never gave anything away as the Champions held on to claim their first win.