The boys were not at the ceremony to collect the award in person but thanked their fans in video clips.
Other stars winning multiple awards included Ariana Grande, 5 Seconds of Summer and Katy Perry, who was also absent from the event.
The event was held at the Hydro arena in Glasgow on November 9.
Anaconda singer Nicki Minaj hosted the awards, as well as performing a medley of some of her biggest hits.
Other performers included U2, Ed Sheeran, Royal Blood and Kiesza, who performed a large part of her set from inside a glittery red phone box.
Alicia Keys was among artists performing at the O2 Academy in Glasgow as part of an outside broadcast. Her performance was shown live on TV screens around the Hydro.
Speaking ahead of the show James Currell, chief operating officer for Viacom International Media, who produce the show, said he hoped this year’s awards could reach even more viewers than in the previous year.
He said: “Tonight millions of viewers from across the world will see us from Glasgow on our 60 MTV channels and our 200 MTV digital properties.
“Last year we had 55 million people see the event. Could we do more tonight? Let’s keep our fingers crossed.”
Organizers revealed that 6,213 miles of cable had been installed to power the event, and a wiggery has been installed backstage to accommodate 500 wigs and 300 hairpieces.
Twenty two hairdressers and 40 make-up artists will assist the acts while 80 costumes have also been prepared.
The dressing rooms contain a number of treats, including a limited edition 10-year-old Highland single malt whisky from Glengoyne.
Meanwhile, each presenter and performer will be given presents including diamond and crystal jewellery, and SpongeBob SquarePants socks.
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