The Canadian singer, who wasn't at the show in the Netherlands, beat Adele to best song for his track Sorry.
Justin Bieber also picked up the biggest fans' title - the third year in a row he's collected it - after a vote on Twitter and Instagram and won in the best Canadian act category.
The ceremony in Rotterdam paid tribute to Prince with purple trophies.
The star died aged 57 in April after being found collapsed in a lift at his home in Minnesota.
Justin Bieber thanked his fans on Twitter.
Justin Bieber didn't have it all his own way though.