Reports emerged on Wednesday that Khumalo would part ways with Amakhosi; the only professional team he played for in South Africa.
When Chiefs asked Khumalo to step aside in 2016, the club said he would take up a role in the academy, but nothing was made official.
The 50-year-old was presented to the media on Thursday afternoon, a day before the start of the new PSL season.
Khumalo will work hand-in-hand with Kgoloko Thobejane and his technical team at Baroka.
Dr Khumalo addressing the media pic.twitter.com/JKHab9cy5b— SAFPU (@SAFPU_Official) August 17, 2017
The former Amakhosi assistant coach brings with him a wealth of experience having been in the coaching circles for over a decade.