Spaniard Marc Marquez, who did not race due to injury, has already wrapped up the title and leads the overall championship standings on 545 points, followed by his brother Alex on 388.
"Making history with Marc at home feels amazing. I am really, really happy," Alex said. "I felt all the nerves during all the races, trying to ride the proper way. (I was) really stiff on the bike. I was just thinking about that."
"But in the end, we made it here - it was a really long season, and finally we're second in the world championship. Now we need to enjoy (it).
"We have three races in front of us to enjoy, to try (new) things for the next year, but especially to enjoy. It is an incredible achievement."
Twice MotoGP champion Bagnaia moved ahead of Marco Bezzecchi for third place in the world championship after his sprint win. The two riders are level on 286 points, but Bagnaia holds the advantage on the countback with more race victories than the Aprilia rider, who finished sixth in the sprint.
Italian Bagnaia led from start to finish at the Sepang International Circuit, crossing the line 2.259 seconds clear of Alex Marquez to secure his second sprint victory of the season, having won the sprint in Japan last month.
Bagnaia, asked if he was back to his best after last weekend's Australian Grand Prix frustration when he was forced to retire following a crash with four laps remaining, said, "I don't have an answer to that, but in any case, happy."
"The team deserves this result because (when) I'm in trouble, they're in trouble too. It's not easy. One week ago, we were struggling. Yesterday as well I was struggling a bit.
"And today I'm competitive. So we just need to figure out what this situation is, because I think no one in the past has ever felt something like this. We just need to focus and try to work like we did this weekend."
Fermin Aldeguer had initially completed the podium after a late charge past KTM's Pedro Acosta, but the Gresini Racing rider was later handed an eight-second penalty for low tyre pressure, dropping him out of the top three.
Despite losing his first MotoGP sprint podium, Spaniard Aldeguer still sealed the Rookie of the Year title after an impressive debut season.