Spaniard Alex Rins won the race in Valencia, while Fabio Quartararo was fourth to finish 17 points behind Bagnaia after blowing a big lead from early in the season.
Quartararo was 91 points ahead after the first nine races.
The 25-year-old Bagnaia won seven races, including four in a row at one point.
“The hardest race of my life,” Bagnaia said. “The most important thing is that we won the championship. It’s a really great day.”
"We did it. I am so happy and super proud because I deserved this victory; Suzuki deserves this victory. During all the weekend I tried to stay calm with all the emotions and all these things, but in the grid in the last minute when you say goodbye to the team members I was crying. "
A Ducati rider hadn’t won a title since Casey Stoner in 2007, and it had been 50 years since an Italian rider had won a MotoGP title with an Italian bike.
Rins’ win at home came in his farewell from Suzuki. It was his fifth MotoGP career win.
Spaniard Augusto Fernández won the Moto2 title.