He appeared in the Springs Magistrates Court on Tuesday.
It happened after a mum discovered that the pastor had allegedly been sleeping with her young daughter and reported the matter to the cops.
The mum told Daily Sun they were still traumatised by the incident.
“What makes matters worse is my daughter is in matric and is struggling to cope,” said the mum.
Pastor Paulos Chapole of the Duduza Ministers Fraternity said: “We applaud the victim’s mum for opening a case against the pastor.
“It seems the suspect has been sleeping with the girl for some time.”
Police spokesman Captain Johannes Ramphora confirmed a case of rape was opened at Springs Police Station and said the suspect was released on bail.
“The case has been postponed to 8 December,” said Ramaphora