In spite of subjecting members to inhumane conditions, Pastor Mnguni seem to command a cult followership.
Opposition Economic Freedom Fighters (EFF) party activists disrupted a service near the capital, Pretoria, and a tent was burnt down in the fracas.
Pastor Penuel Mnguni gained notoriety after photos showed him dangling a live snake into a man's mouth.
However, police withdrew charges of animal cruelty against him.
Police spokesman Mathews Nkoadi said in July that there were no witness statements and insufficient evidence to bring a case.
Dubbed the "snake pastor", Mr Mnguni runs the End Times Disciples Ministries in Soshanguve, north of Pretoria.
The EFF said that they had raided a service on Sunday because they wanted Mr Mnguni to "lead by example" and eat snakes and rats.
But EFF spokesman Mbuyiseni Ndlozi nevertheless tweeted that the pastor "ran away" so they were unable to confront him. Mr Mnguni has not commented on the raid.
