Yamaha's defending champion Quartararo was 23 points behind Bagnaia heading into the final race on Sunday, needing a victory and a victory only to leapfrog the Italian, but he could only finish fourth in a race won by Suzuki's Alex Rins.
Bagnaia came ninth, allowing him to to retain his lead in the championship and give Ducati their first title since Casey Stoner won it in 2007, ending 15 years of dominance from Japanese manufacturers.
But there was disappointment for his Ducati teammate, Australian Jack Miller, who failed to finish his final race for the team after a five-year spell before he moves to KTM next season.
The driver from Townsville, who slid out on lap 23 while lying fourth, is ending the season in fifth place overall, 77 points behind the champion.
Bagnaia's title, however, marked the greatest comeback in MotoGP history as he was 91 points down midway through the season and it ended a 50-year wait for an Italian rider to win the championship on an Italian bike.
Bagnaia celebrated by waving the Italian flag as Ducati presented him with a golden helmet, the visibly emotional 25-year-old taking a moment to compose himself before raising it in the air in celebration.
― With AAP.
