Pirates had Ben Motshwari back from suspension and recalled goalkeeper Wayne Sandilands from the loss to TS Galaxy on Sunday while Happy Jele was also handed a long-awaited return.
Pirates felt the pressure right from the get go and were unfortunate not to go behind from a one-on-one by Evidence Makgopa, but Sandilands rose up with a solid save.
The host began to feel the brunt of the Buccaneers towards the half-hour mark with a thumping shot from Siphesihle Ndlovu shaved the top of Oscarine Masuluke's goal.
Then, a forced injury resulted in the Buccaneers bringing on Fortune Makaringe nine minutes before the halftime period in the place of the departed Motshwari.
Bakgaga Ba Ga Mphahelele stunned the visitors through when Denwin Farmer finished off a loose ball from a free-kick past Sandilands after Bucs failed to clear their lines.
The Buccaneers pulled level just before the break through a smart finish from a free-kick by Mhango.
Bakgaga rang the changes ahead of the second half, as Joslin Kamatuka came on for Richard Mbulu, whilst Masuluke thwarted Mhango from a miscommunication at the back.
The Buccaneers continued to pose all the questions at the host midway following the second half, with a header from a set-piece by Jele and a clever attempt by Vincent Pule.
Farmer went close to a double 12 minutes to the end courtesy of a loose effort, but Sandilands smothered the centre-back.
Pirates grabbed the lead with two minutes to go through a header from Terrence Dzvukamanja off a telling cross from Wayde Jooste to see out the clash in the end.
Baroka: Masuluke, Kgoetyane, Gebhardt, Farmer, Jampies, Makume, Mbulu, Mosele, Mgaga, Kambala, Makgopa.
Subs: Chipezeze, Seema, Mogale, Shozi, Mahlonoko, Monama, Nkhona, Mphahlele, Kamatuka.
Pirates: Sandilands, Jele, Nyauza, Maela, Jooste, Ndlovu, Motshwari, Lorch, Pule, Mhango, Hotto
Subs: Sithole, Mako, Sam, Hlatshwayo, Makaringe, Mntambo, Zungu, Dlamini, Dzvukamanja