Bagnaia and Pramac title rival Jorge Martin came into the championship decider in Valencia split by 14 points after the latter won the sprint on Saturday.
But the championship battle came to a halt on lap six of the grand prix when Martin collided with Honda's Marc Marquez, on the eight-time world champion's final appearance for the team, while battling for fifth.
Bagnaia went on to win the race for his second title in a row, becoming the first rider since Marquez to win consecutive titles and the first since Mick Doohan to defend his number one plate.
Asked how he felt about that fact, Bagnaia said: "I feel well, it's fantastic. I think many times this season the only two able to win were Marc and Vale, and all the races where we were struggling more to do it.
"And even more with the number one, finishing second in the championship could be a very bad result.
"I couldn't be happy with a second position in the championship, because a number one plate means that you need to demonstrate that you are the number one and I think we did everything perfect to be considered the number ones.
"Even more in the second part of the championship, because we were the faster many times but we managed always to be competitive and faster and stronger on Sunday, that is the main race, the race that gives to you more points.
"Last season was a season to be very proud, but this season even more because the number one plate with many mistakes, bad luck in some situations and we won the title the same. So we have to be very proud."
Source: Autosport