The 53-year-old tactician was placed under suspension by the club for alleged insubordination last month.
The Limpopo-based side has now dismissed Kerr, who had joined the club in December 2019 when he replaced Zambian coach Wedson Nyirenda.
"Baroka FC parted ways with team head coach," a club statement read.
Meanwhile, Baroka also confirmed that Kerr has been replaced by Thoka Matsimela as the new club head coach.
"Baroka FC's newly appointed head coach for 2020/2021 season Thoka Matsimela," a club statement read.
Matsimela was thrilled to be given the opportunity to lead the 2018 Telkom Knockout Cup champions.
"Firstly, let me say thanks for this opportunity, my chairman. He gave me the opportunity to lead the team as the coach of Baroka FC," Matsimela said.
"I am humbled by the opportunity. I will make sure that I grab this opportunity with two hands."
Matsimela worked as the assistant coach under Mike Rapatsa‚ Sello Chokoe‚ Kgoloko Thobejane‚ MacDonald Makhubedu, Nyirenda and Kerr at Baroka over the years.
The loyal tactician is confident of guiding Bakgaga Ba Mphahlele to a top-eight finish which would see the team qualify for the MTN8 for the first time.
"Yeah, we have been given a mandate of making sure that the team finishes in the top eight this season," he continued.
"It is something we have been failing to achieve as a club. We have been unable to secure a top-eight finish in the previous seasons.
"But we promise that Baroka FC will compete in the MTN8 next season."
Matsimela took charge of Baroka's first three matches this season after Kerr was placed under suspension.
As a result, Bakgaga Ba Mphahlele are placed second on the PSL standings with seven points from three games.