For his first set, Bieber sang inside an overgrown, moody barn set, complete with a neon cross which set the tone for his powerful performance of "Holy."
Bieber was joined on stage by his collaborator on the track, Chance the Rapper -- who previously served as an SNL musical guest and host last year.
Bieber appeared to be overwhelmed with emotion as the song came to a close and he bent over at the waist as the number ended. Chance smiled and supportively embraced Bieber as the show went to commercial.
The pop icon wasn't the only one who got emotional over the performance. Many fans took to Twitter to shower the singer with praise.
Bieber's second performance of the night was even more powerful and heart-wrenching. The unique number began in his green room -- instead of on a stage -- as he sang the opening, painful lines of his new song "Lonely" into a mirror.
The camera followed Bieber as he sang while walking backstage through the halls of the studio. He delivered a flawless and incredibly touching set as he came out from backstage and slowly walked into the spotlight, ending the performance in front of the audience -- who responded with thunderous applause.
ET learned on Thursday that the "Holy" singer went in to start rehearsing for this weekend’s SNL. ET also learned that every staff member at the studio is taking daily COVID-19 tests and that there are COVID compliance officers walking around to make sure people are obeying all the guidelines and social distancing rules.
SNL airs live, coast-to-coast, on Saturdays at 11:30 p.m. ET, 8:30 p.m. PT on NBC.