"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.
He noted that he first watched Eminem when he was just three years old.
Bieber called Usher "not only my mentor, but my best friend and my big brother." The two hugged and shared the stage as the three-hour-long show neared an end.
Bieber also won the breakthrough artist and favorite album awards.
Apparently running out of new people to thank in his acceptance speeches, Bieber mentioned the king of pop. "I want to thank Michael Jackson, because without Michael Jackson none of us would be here," Bieber said.
Usher took home two awards of his own, including for favorite male soul or R&B artist. "Can't call it a comeback," Usher said. "I've been doing it 18 years, ya'll."
A music awards show seems incomplete without unplanned onstage antics. Rapper Nicki Minaj provided the closest thing to that this year when she interrupted the announcement of favorite soul or R&B female artist to plug her upcoming album release.
Rihanna, the category's winner, graciously ignored the slight and even complimented Minaj for her green hair.
Taylor Swift, who was last year's big winner with five awards, only won favorite country female artist this year. "I only want to thank the fans," Swift said. "You guys get me, and you know where I'm coming from."
Brad Paisley won the favorite country male artist award, a trophy he also carried home in 2008.
Other winners included:
-- Lady Antebellum, favorite country band, duo or group
-- Black Eyed Peas, favorite pop or rock band, duo or group
-- Muse, favorite alternative rock artist
-- Shakira, favorite Latin music artist
-- Michael Buble, favorite adult contemporary artist