Pastor Mboro’s Incredible Happenings Church was set alight by angry schoolchildren.
The day before, a widely circulated video appeared to show MBORO, real name Paseka Motsoeneng, waving blades during a tense stand-off with teachers in Katlehong, a township just outside Johannesburg.
He is flanked by a man carrying what police have since identified as a replica firearm.
Provincial authorities said the two young children filmed being removed are at the centre of a custody battle after their mother passed away.
Five people were arrested following the incident at the school.