"This is big," said the 16-year-old Canadian, whose first single hit the charts barely 18 months ago.
Fans voting online chose Bieber over Eminem, Ke$ha, Lady Gaga and Katy Perry for the night's top honor.
Bieber also out-polled Usher, who helped launch and guide his career, and Eminem to win the favorite rock or pop male artist award.
Bieber called Usher "not only my mentor, but my best friend and my big brother."
- Favorite Soul/R&B Album: Usher, Raymond v. Raymond
- Favorite Pop Rock Band/Duo/Group: The Black Eyed Peas
- Favorite Country Female Artist: Taylor Swift
- Favorite Latin Music Artist: Shakira
- Favorite Soul/R&B Female Artist: Rihanna
- Favorite Country Male Artist: Brad Paisley
- Favorite Breakthrough Artist: Justin Bieber
- Favorite Pop/Rock Male Artist: Justin Bieber
- Favorite Country Band/Duo/Group: Lady Antebellum
Favorite Alternative Rock Music Artist: Muse
- Favorite Adult Contemporary Music Artist: Michael Bublé
- Favorite Soul/R&B Male Artist: Usher
- Favorite Artist of the Year: Justin Bieber
- Favorite Country Album: Carrie Underwood, Play On
- Favorite Rap/Hip-Hop Male Artist: Eminem
- Favorite Pop/Rock Album: Justin Bieber, My World 2.0
- Favorite Pop/Rock Female Artist: Lady Gaga
- Favorite Contemporary Inspirational Artist: MercyMe
- Favorite Rap/Hip-Hop Album: Eminem, Recovery
- Favorite Soundtrack Album: Glee: The Music, Volume 3 Showstoppers