Motsoeneng, wielding a panga, forcefully took his two grandchildren from the Matsediso Primary School in Katlehong, south-east of Johannesburg, on Monday.
The incident, captured on cellphone footage went viral on social media and led to his tent church being razed to the ground the following day.
The charismatic preacher, his son Vincent Revival Motsoeneng, 27, and bodyguard Clement Camillot Baloyi, 43, were not asked to plead and were remanded in custody pending a bail hearing scheduled for Friday next week.
The trio are facing a variety of charges, including assault, handling a firearm recklessly that could endanger lives and property, rendering security services while not registered, malicious damage to property, assault and intimidation.
Outside the courtroom, members of the maternal family of the children shouted "finally".
A small group of community members sang and chanted against Motsoeneng and proclaimed their support for the family.
Neighbour Mapule Mauku, who was among the members, expressed the community's shock and concern for the family.
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