Bieber, just 18, also won Favorite Pop/Rock Male Artist and Favorite Pop/Rock Album for "Believe."
Carly Rae Jepsen was proclaimed New Artist of the Year, MTV reported.
Taylor Swift won for Favorite Country Female Artist and Minaj earned Favorite Rap/Hip-Hop Artist and Favorite Rap/Hip-Hop Album ("Pink Friday: Roman Reloaded").
Luke Bryan won Favorite Country Male Artist, while Lady Antebellum was named Favorite Country Band, Duo or Group.
Carrie Underwood took home the award for Favorite Country Album ("Blown Away").
Usher won Favorite Soul/R&B Male Artist, while the Favorite Alternative Rock award went to Linkin Park.
David Guetta took the Favorite Electronic Dance Music Artist honor.