Timberlake won video of the year for Mirrors and collected the lifetime achievement award.
One Direction picked up song of the summer for Best Song Ever at the Brooklyn event.
But it was former Disney star Miley Cyrus who sparked a social media storm following her raunchy performance.
The 20-year-old shrugged off her Hannah Montana squeaky clean image by stripping down to a nude-coloured latex bikini, sporting a giant foam finger and dancing provocatively with R&B singer Robin Thicke as he sang Blurred Lines.
She also performed surrounded by giant bears as she sang her number one hit single We Can't Stop.