The pop superstar took home the Michael Jackson Video Vanguard Award, Video of the Year for Mirrors, which also claimed Best Editing honours, and his Suit & Tie promo earned the Best Direction prize.
He also wowed with a show-stopping performance featuring a medley of his solo hits and a brief 'N Sync reunion.
Rap duo MACklemore & Ryan Lewis were also big winners - they scored Best Hip Hop Video and Best Cinematography trophies for their Can't Hold Us promo and also landed the night's Best Video with a Social Message award for their gay anthem Same Love, which they performed with Mary Lambert and special guest Jennifer Hudson.
Lady Gaga kicked off the ceremony at the Barclays Center in typical bizarre fashion, dressed as a futuristic Mother Superior. The Paparazzi singer began her performance of new single Applause wearing a weird white nun's habit but the get-up was quickly ripped off her by dancers to reveal a glittery black leotard with matching skull cap.
That outfit became a shimmering blue two-piece, topped by a peroxide white wig. The pop superstar also donned a canary yellow wig and face paint during the opening performance, and wrapped it up following a quick change, dashing out in a two-piece bikini and long blonde shaggy hairpiece.
Other performance highlights included Miley Cyrus, who performed We Can't Stop surrounded by dancing teddy bears, while wearing a fluffy grey bodice. She also sported a new hairstyle - tight cat-ear-like bunches on top and a short ponytail.
The former child star then proved she's all grown up by ripping off her top to reveal orange rubber bra and panties as she took part in a performance of Robin Thicke's Blurred Lines. The hitmaker strutted out on stage wearing the thick-striped black and white suit.
During the pair's suggestive routine, Cyrus donned a large foam hand to feel Thicke up with and then bent over and wiggled her backside into the singer's crotch while smiling with her tongue hanging out.
After watching Cyrus dancing with Thicke, comedian Kevin Hart joked, "Miley better go and get a damn pregnancy test after doing all that grinding."
Kanye West, Justin Timberlake, Bruno Mars, MACklemore & Ryan Lewis, and Drake also hit the Barclays Center stage, while Katy Perry closed the 2013 ceremony by performing her new song Roar from underneath the Brooklyn Bridge.
The full list of 2013 Mtv Vmas winners is:
Video of the Year - Mirrors by Justin Timberlake
Best Hip-Hop Video - Can't Hold Us by MACklemore & Ryan Lewis featuring Ray Dalton
Best Male Video - Locked Out of Heaven by Bruno Mars
Best Female Video - I Knew You Were Trouble by Taylor Swift
Best Pop Video - Come & Get It by Selena Gomez
Artist to Watch - Austin Mahone
Best Collaboration - Just Give Me a Reason by Pink featuring Nate Ruess
Best Video with a Social Message - Same Love by MACklemore & Ryan Lewis featuring Mary Lambert
Best Rock Video - Up in the Air by 30 Seconds to Mars
Best Art Direction - Q.U.E.E.N by Janelle Monae featuring Erykah Badu
Best Choreography - Treasure by Bruno Mars
Best Cinematography - Can't Hold Us bu MACklemore & Ryan Lewis featuring Ray Dalton
Best Direction - Suit & Tie by Justin Timberlake featuring Jay Z
Best Editing - Mirrors by Justin Timberlake
Best Visual Effects - Safe & Sound by Capital Cities
Best Song of the Summer - Best Song Ever by One Direction
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