Bakgaga won the Premiership game 2-1, with Chiefs coach Steve Komphela needing a police escort afterwards as unruly fans hurled missiles at Moses Mabhida Stadium.
The PSL have since charged the Soweto giants with failing to provide adequate security, while Amakhosi midfielder Willard Katsande is also in trouble for allegedly entering the technical area despite being suspended.
Baroka, meanwhile, have been charged for arriving late at a mandatory pre-match meeting.
The league released a statement, which reads: 'The following matters will appear before the Premier Soccer League Disciplinary Committee tonight, 07 November 2017.
'BAROKA FC: The club has been charged with contravening the Compliance Manual after the club's representative failed to arrive on time at the mandatory pre-match meeting ahead of their fixture against Kaizer Chiefs at Moses Mabhida Stadium 30 September 2017.
'KAIZER CHIEFS: The club has been charged with failure to provide adequate security at their fixture against Baroka FC at the Moses Mabhida Stadium on 30 September 2017 leading to a section of fans throwing objects on the field.
'KAIZER CHIEFS and WILLARD KATSANDE: The club and Mr Katsande have been charged with contravening the Compliance Manual after Mr Katsande entered the technical area although he was suspended.'