Police said he was assaulted during a burglary at St Peter's Cathedral in the Divis Area of the city.
Detectives are hunting two men, one who was believed to have been armed, who stormed the church at 9.30 on Monday night.
A sum of money was stolen during the incident.
The priest was given treatment for his injuries.
Police are appealing for information.
In a statement the Diocese of Down and Connor said: "The priest has been left very distressed and traumatised by this experience. The level of organisation and aggression perpetrated by these robbers is particularly disturbing and deeply concerning.
"He is recovering and has received many messages of support from parishioners, clergy and the local community. He is assisting the PSNI with their investigations."
"We would ask for vigilance and encourage anyone who has information in relation to this incident to bring it to the attention of the detectives at Musgrave PSNI Station."