As Long As You Love Me singer Bieber - who was unable to attend the event as he has a concert in Brooklyn tomorrow and is due to meet Selena Gomez for crisis talks following their split last week - picked up Best Male, Best Pop and Best World Stage.
Other big winners included One Direction, who won Best New and Biggest Fans and Carly Rae Jepsen who picked up Best Song for Call Me Maybe and also inspired a fan invasion during her performance of her chart-topping hit.
After the show, the 26-year-old star admitted: "My speech was horrible. I wasn't expecting to win and as you could tell - was very unprepared, I think I said thank you a million times. And I could say them a million more before I would be done.
"I'm loving being able to share my music, it's been a dream of mine since I was 7 years old and to live that out, its kind of a Cinderella story to me, I feel very lucky."
Korean pop sensation Psy's was awarded Best Video for his global hit Gangnam Style which he performed on stage with an army of look-a-like dancers and included a special cameo by David 'The Hoff' Hasselhoff.
Other performers included British R.I.P singer Rita Ora who kicked off the evening's festivities by performing the song as she descended from the rafters in a giant bird cage, as well as Alicia Keys, indie rockers fun, The Killers, Muse and No Doubt who blew away the audience with their amazing live performance of 'Looking Hot'.
The '2012 MTV EMA' award winners are:
Best female
Taylor Swift
Best song
Carly Rae Jepsen - "Call Me Maybe"
Best male
Justin Bieber
Best live
Taylor Swift
Best look
Taylor Swift
Global icon
Whitney Houston
Best video
PSY - "Gangnam Style"
Best world stage
Justin Bieber
Best push
Carly Rae Jepsen
Best alternative
Lana Del Rey
Best electronic
David Guetta
Best hip-hop
Nicki Minaj
Best new
One Direction
Best pop
Justin Bieber
Best rock
Linkin Park
