Crown prosecutor Michael Walker told the court that Sister Leva was one of the teachers leading a group practice of an action song at St Patrick's Catholic Church in Panmure in April last year.
Sister Leva began yelling at the 9-year-old girl, telling her she was doing the actions incorrectly.
"She went up to her and flicked her in the side of the head, causing her to feel dizzy," Walker said.
"She then twisted her arm up behind her back and the girl heard a click in her shoulder and neck."
The next day the girl's mother took her to hospital. where the fracture was discovered.
A church source said Sister Fono, who was from Tonga, was not a fulltime staff member and no longer worked at the church.