In a field that included superstar Taylor Swift, who had the most nominations of the night, the Seattle-based duo won for Best Video with Downtown.
“I had no idea we were going to win an award,” Macklemore told the gala ceremony in Milan.
“We’re not on a major label; we don’t have a big budget. What you guys give to us, we give back to you in the art we make,” Macklemore said, referring to fans.
The duo, best known for their 2012 gay equality anthem Same Love shot the video for the funky trackDowntownin Spokane, Washington, showing street life as Macklemore shops for a moped and leads a street parade.
Pop sensation Bieber, whose long-awaited fourth album Purpose comes out next month, appeared in a red jumpsuit as he performed his new hit What Do You Mean?driven by a mellow electronic beat.
The Canadian singer took home awards for Best Male, Best Collaboration and Best Look – for which he joked, “I got these looks from my mum.”
Bieber hinted that he was happy to win attention for his music, not his legal troubles or often turbulent personal life.
“Thank you, it’s been a long couple of years. I just feel that this is pretty awesome to be recognised for my music,” Bieber said.
Best Video is determined by MTV’s editorial team, but most categories are decided through fans’ voting.
Best Song went to Taylor Swift’s Bad Blood,whose video – a starstudded action clip with feminist undertones – landed Video of the Year at the main US-based MTV awards in August.
R&B star Rihanna, who is also preparing to release a long-awaited album, won Best Female and British boy band One Direction scored in the Best Pop category.
Nicki Minaj won in the hip-hop category, as she did at the main MTV Video Music Awards in Los Angeles in August.