The rapper won the Best Hip Hop prize and was awarded the the Global Icon trophy for his continued success over the last decade. He has now won 15 MTV Emas - more than anyone else.
He also took to the stage to perform Berzerk and Rap God before Will Ferrell, dressed as his Anchorman character Ron Burgundy, presented him with his Global Icon accolade.
Justin Timberlake and MACklemore & Ryan Lewis had led nominations ahead of the ceremony, but Timberlake went home empty handed, while the hitmaking duo had to make do with the prize for Best New Act.
Miley Cyrus stole the spotlight during the ceremony - the former Hannah Montana star performed twice, opening the event with a rendition of her We Can't Stop hit accompanied by a leather-clad little person, who she groped and spanked. Miley then returned to the stage for an impassioned performance of Wrecking Ball, which won her the Best Video award.
Her pal Katy Perry scooped the award for Best Female and performed her new track Unconditionally, while and absent Justin Bieber was named Best Male for the second year in a row. He accepted his award via a video link from South America, where he is currently on tour.
Other performance highlights came from Kings Of Leon, The Killers, Icona Pop, Robin Thicke, Snoop Dogg, Katy Perry and Bruno Mars.
Will Ferrell's Ron Burgundy character appeared in a number of skits throughout the night, guiding the viewers around Amsterdam with a canal trip accompanied by Daft Punk lookalikes and making a confused visit to the city's famous red light district.
LMFAO star Redfoo hosted the evening and donned nine different costumes, including one which appeared to be edible.
The full list of winners is as follows:
Best Song: Bruno Mars - Locked Out Of Heaven
Best Female: Katy Perry
Best Male: Justin Bieber
Best Pop: Justin Bieber
Best New Act: MACklemore & Ryan Lewis
Best Live Act: Beyonce
Best Hip Hop: Eminem
Best Rock: Green Day
Best Electronic: Avicii
Best Alternative: Thirty Seconds To Mars
Best Video: MIley Cyrus - Wrecking Ball
Best Look: Harry Styles
Best World Stage: Linkin Park - Mexico 2012
Biggest Fans: Tokio Hotel
Best Push: Austin Mahone - April 2013
Best Worldwide Act: Chris Lee, China
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