Makhubedu has been in charge of the team since Thobejane was suspended.
Thobejane was fired following a hearing where he was found guilty and subsequently asked to vacate his head coach position.
Baroka FC CEO Morgan Mmamilla says the club is not looking for a new coach and the club trust Makhubedu with the team.
“Looking for another coach would be an insult to MacDonald, for now he will be in charge,” Baroka FC CEO Morgan Mmamilla told Phakaaatthi.
“If a coach can play five games, win two and draw three then what more do you want, we only conceded two, he is far much better than other coaches. If he continues to do well then he will be the head coach next season.”