The 17-year-old thanked his fans and family for their support as he claimed the Best Male and Best Pop awards at the end of a week that has seen him the centre of lurid allegations.
“You guys are the reason I am on stage right now,” he said, before rubbishing internet rumours about him as “crap”.
Bieber on Wednesday vowed “vigorous” legal action after a 20-year-old reportedly claimed he fathered her baby, saying the assertion was “malicious” and demonstrably false.
The teen-heartthrob was also awarded the MTV Voices Award at a dinner on Saturday in recognition of his charity work.
Shock-pop icon Lady Gaga was the night’s big winner, showing up in person at the Northern Irish capital’s Odyssey Arena to claim the Best Female, Best Song, Best Video and Biggest Fan awards.
Hosts David Hasselhoff and Selena Gomez — Bieber’s girlfriend — presented the awards to Lady Gaga, who was dressed in an eye-catching fan-like outfit, complete with extravagant headdress which obscured the singer’s face.
Fellow American Katy Perry called her Best Live Act prize “amazing”.
“I just played at this arena ten days ago,” she added. “This is my favourite award because my fans mean so much to me.”
German sensation Lena fought off competition from British soul diva Adele in the race for the Best European Act but lost out to South Korea’s Big Bang in the Best Worldwide Act category.
British rockers Coldplay kicked off the ceremony with a performance of “Every Teardrop Is A Waterfall”, urging the crowd to “shout for Justin Bieber.”
Flamboyant British group Queen were hounoured with the Global Icon award, which was presented to them by Katy Perry.
“They changed my life. The legacy of Freddy Mercury will forever be burning in the skies at 200 degrees,” she said before introducing band members Brian May and Roger Taylor.
The current Queen line-up closed the show with a medley of their hits, while California veterans The Red Hot Chili Peppers played live from the city’s renowned Ulster Hall.
Rapper Eminem took the award for Best Hip Hop Act, but was unable to attend Sunday’s ceremony.