Paintsil's contract was due to expire in June 2018.
Steve Komphela brought Paintsil to Amakhosi when he was appointed head coach two years ago, having worked with the ex-Ghana international at former club Maritzburg United.
Chiefs released a statement, which reads: 'Kaizer Chiefs and John Paintsil have come to an agreement to terminate his contract as the assistant coach of the Club with effect from 6 June 2017. His contract was due to expire in June 2018.
'Both parties have signed a separation agreement, the terms of which are confidential.
'The club thanks John for his contribution and wish him well for his future endeavours.'