The incident, which occurred in 2016, has resurfaced thanks to a number of recent viral social media posts.
Tupac's Hail Mary contains lyrics about violence, female genitalia and the N-word.
The traditional words are "Hail Mary full of grace, the Lord is with thee". However, Tupac's version asks Mary "do you want to ride or die?"
Father Da Silva apologised for the mix-up saying a young boy, who was in charge of providing the lyrics, accidentally downloaded the wrong song sheet.
"The page was in the middle of the booklet. When people looked at this page, they saw it before the start of the show. Two people saw it and alerted us to it."
"We are very sorry to say that this happened."