KickOff.com yesterday reported the Kaizer Chiefs icon had left Bakgaga, who previously indicated Khumalo's future was hanging in the balance following the appointment of new coach Wedson Nyirenda a fortnight ago.
Khumalo, who shocked many when he previously severed ties with the Glamour Boys, ended last season as interim coach of Baroka following the removal of Kgoloko Thobejane and MacDonald Makhubedu from the hotseat.
Baroka released a statement, which reads: 'After months of speculation Doctor Khumalo and Baroka FC have finally agreed to go separate ways.
'We have recently acquired the service of the head coach and the club had to consider doing away with the position of technical director in order to maintain our financial health state.
'We can't discount the fact that Doctor Khumalo was given the club value we never had and we will forever be grateful to him.
'It is in this spirit to thank him for choosing us when he left Kaizer Chiefs a year ago.
'As Baroka Football Club, we will like to wish Doctor Khumalo all the best in his future endeavours.'
Former Chiefs striker Nyirenda will be assisted by Fani Mthethwa and goalkeeper coach Thomas 'Spaghetti' Mare in the new season.