The hosts came into the clash on the back of a loss to AmaZulu, while the Citizens comfortably saw off SuperSport United in Cape Town.
Baroka took an early lead through Mpho Kgaswane who finished from close range on six minutes after some poor marking by the City defence.
It was never going to be an easy task for them facing a side who got the better of them in the corresponding fixture last season.
Matters worsened for them, as Bakgaga doubled their tally through the boot Matome Kgoetyane on 19 minutes via another dead-ball situation.
City made the first change early in the second half, bringing on Siphelele Mthembu for Surprise Ralani. It was to be Mthembu reducing the deficit, finishing off from close range on 48 minutes.
The Citizens tried to get back into the contest, but woeful finishing upfront didn’t aid their cause leaving Polokwane with no points in the bag.