Eminem, who was not at Sunday’s ceremony, won artist of the year, the night’s top prize.
Bieber thanked “everybody who helped me get out of my home town” at the event – the first televised BMAs since 2006.
Britain’s Taio Cruz won best single for Dynamite, while other winners included Katy Perry, U2 and Beyonce Knowles.
Eminem’s prizes included top artist and top male artist, while Bieber counted fan favourite and top new artist awards among his haul.
A star-studded ceremony, broadcast live on US TV, was opened by Britney Spears and Rihanna singing a remix of the latter’s hit S&M.
Other performers included Cee Lo Green, country star Keith Urban and Neil Diamond, who sang his 1969 hit Sweet Caroline after winning the icon award.
Beyonce was given the Millennium Award for her musical influence and was also recognised as a role model for women.
U2 won the top touring award for their 360 Degrees Tour.
The awards’ winners were chosen for their popularity, based both on chart performances and internet social and streaming activity.
