The game got off in swift action, where Baroka went on the front foot through Talent Chawapihwa, who saw his shot cleared off the line.
They came close again minutes later with Gift Motupa finding space in the box, only to fail his attempted overhead volley.
The midfielder missed another clear opportunity, this time from a free-kick that saw him head over the top amongst a cluster of defenders.
After relentless pressure, the home side finally got their dues in the 11th minute through Robin Ngalande.
The Atletico Madrid product capitalised on poor handling by George Chigova to poke home his first goal for the club.
With their first shot of the game, Polokwane found themselves level pegging, albeit from the spot by Rodney Ramagalela for his 10th goal of the season following a handball by Mathari Mothupa inside 24 minutes.
That set them up to take the game by the scruff of its neck, and they did that after Sammy Seabi managed to force Ayanda Dlamini to an expert one-handed save after the half an hour mark.
In the second half, Baroka were looking to get back in front and came close after Mpho Kgaswane fired into the side-netting from Motupa’s ball.
City launched threats of their own and nearly found the breakthrough but Ramagalela failed to make proper contact with Seabi’s cross from the right.
At the rate play went about in the opening quarter of the second half, it was headed for another draw but Letladi Madubanya was hoping to abort that but could only fire wide after 66 minutes.
The former SuperSport United and Platinum Stars man launched another attempt at goal, but he headed aimlessly at Dlamini.
In added time, Tebogo Sodi thought he had sealed the victory only for the officials to correctly disallow the goal for offside.