Lieutenant Colonel Priscilla Naidu said the 22-year-old priest and four of his congregants were arrested on Wednesday.
Naidu said they killed the 7-year-old girl while conducting a violent exorcism a week ago.
"The parents and the church members felt that the child was demonised [possessed] and needed prayer," said Naidu.
During the exorcism, they realised the girl needed medical attention and tried to take her to hospital, but she died on the way there.
A post-mortem revealed that she had sustained internal injuries.
Naidu said that on the night of the girl's death, police found bruises on her body and had noted that her eyes were swollen.
"It is suspected that for that hour or two, the girl must have been pushed back and forth while she was being prayed for," she said.
The five men arrested were expected to appear in the Humansdorp Magistrate's Court on Thursday.
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