The blunder occurred when the church accidentally printed the words to the late rapper's "Hail Mary" instead of the traditional prayer.
The song's profane lyrics contain repeated uses of the N-word and the word f***, and lines such as "Revenge is like the sweetest joy next to gettin' p****".
Photos of the printed lyrics and the front of the booklet, titled "Joy to the world 2016: A festival of music for peace & harmony", went viral after they were posted online.
Andrew Choksy, who snapped the photos at the church in Colombo, Sri Lanka, told Mashable : "A lot of people around us were in shock as to whether it was a joke or someone would actually rap the song.
"A few of the older ladies in front of us could not stop looking at the printed booklet."
He found the episode amusing and said the event's organisers did not tell churchgoers how the rude lyrics ended up in the booklet.
The Christmas carol service was a fundraiser for programmes which help the poor.
Father Da Silva, from the archdiocese, told CNN that the mistake was made by a "young boy" who had downloaded and printed the wrong lyrics.
He said organisers asked for the booklets back once they realised the mistake, adding: "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."
Tupac's "Hail Mary" was a collaboration released in 1997 just months after the 25-year-old was gunned down in a still-unsolved murder after watching a Mike Tyson fight in Las Vegas.