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.
MotoGP champion Ducati Lenovo\'s Francesco Bagnaia celebrates with Moto2 champion Red Bull KTM Ajo\'s Augusto Fernandez and Moto3 champion Gaviota GASGAS Aspar Team\'s Izan Guevara