The Canadian singer, 26, shared pictures from the ceremony, showing the couple holding hands while being submerged underwater.
“This was one of most special moments of my life,” Bieber said. “Confessing our love and trust in Jesus publicly with our friends and family.”
The ceremony was carried out by pastor Judah Smith.
Bieber married model Hailey, 23, in 2018 and they have both said their Christian faith is central to the relationship.
Speaking earlier this year while answering fan questions on his The Biebers on Watch series, the singer said he wished he had saved himself for marriage.
“There are probably a lot of things I would change,” the pop superstar said. “I don’t regret anything because I think it makes you who you are, and you learn from things.
“If I could go back and not have to face some of the bad hurt that I went through, I probably would’ve saved myself for marriage.”
Bieber added: “I know this sounds crazy. Sex can be kind of confusing when you’re being sexually active with anybody … I would have probably saved myself for marriage.”