Canada's Olympic women's curling team accepted the award on Bieber's behalf, but didn't mention the boos.
When Canadian singer Serena Ryder picked up her award for songwriter of the year, she used some of her onstage time to defend the 20-year-old pop star.
"I really think that Justin Bieber is an amazing musician and he deserves every bit of that award,” she said. "He’s been working his ass off his entire life and we need to support how awesome he is. I’m not just trying to kiss ass. He’s amazing."
Despite the jeers, Bieber seemed enthusiastic about his win on Twitter.
"We won #JUNOFanChoice for the 4th year in a row! Love to all my beliebers. Thank u. Love u," he tweeted Sunday.