"I wanted to thank you for always believing in me," Bieber said, looking to his mom.
The 18-year-old also won awards for favorite pop/rock male artist and favorite pop/rock album for "Believe."
Usher also took home a trophy for favorite soul/R&B male. He also happens to be Bieber's mentor.
"The longer you do it, the more of an example you can set," Usher said. "Being able to be that to him, being a mentor and just being an artist who continues to evolve and find my way, find my voice and find my audience, that is the example I think that he's following."
Bieber himself has become a mentor to this year's best new artist, Carly Rae Jepsen.
Nicki Minaj picked up two trophies for favorite rap/hip-hop artist and album.
In the world of country, Lady Antebellum won favorite group, Luke Bryan won favorite country male artist and Carrie Underwood for favorite album.
Korean pop star Psy of "Gangnam Style" fame and his special guest MC Hammer brought the house down when they closed the show. They danced to a "Gangnam Style" and "2 Legit 2 Quit" mash-up in Hammer pants.
Hammer reflected that Psy's "Gangnam Style" joins James Brown, Michael Jackson and his own "Hammer Time" as timeless dance moments.
"To be with somebody who has shifted the planet and had fun and (be a) very humble and respectable guy, I loved doing it and we had a great time together," Hammer said.
The Associated Press contributed to this report.