Saturday's service at Newark's Cathedral Basilica of the Sacred Heart was to commemorate the life of baseball star Roberto Clemente.
During the mass Charles Miller, 48, got up from his pew and walked up to the altar where Fr Manuel Cruz was delivering the service.
According to NJ.com, Miller then allegedly punched the auxiliary bishop in the mouth. The force caused Fr Cruz, 63, to fall backwards into the altar.
He received treatment at hospital for his injuries and is now recovering at home.
Essex County Sheriff's spokesman Kevin Lynch confirmed to local media that Miller had been arrested and charged with assault.
James Goodness, spokesman for the Archdiocese of Newark, also confirmed Fr Cruz had been assaulted.
"We are thankful that law enforcement officers were able to apprehend the assailant," Goodness said.
"This is not something that we expect to happen in any of our churches."