The Ducati rider, whose only MotoGP win to date was at the 2009 British Grand Prix, termed Sunday’s win as the biggest of his career.
Though Dovizioso started on pole, he struggled to adjust to wet conditions following a downpour before the race start. The Italian found himself getting overtaken by a number of riders at the start.
The highlight of the first 10 laps of the race was a thrilling encounter between Yamaha rider Valentino Rossi and Dovizioso's Ducati teammate Andrea Iannone.
The two changed leads repeatedly till Iannone crashed out with seven laps left.
In the meantime, Dovizioso steadily climbed up places and was on Rossi’s tail at the end of the Rossi-Iannone duel. With six laps left, Dovizioso took the lead back from Rossi and quickly opened up a big gap, eventually finishing the race more than three seconds ahead of Rossi.
Rossi had some consolation as he clinched second place in the 2016 world championship over his Yamaha teammate and rival Jorge Lorenzo who finished third in Sepang.
Honda's Marc Marquez, who crashed but came back to finish in 11th place, had already wrapped up the championship two weeks ago.
Last week’s winner in Australia Cal Crutchlow too crashed out of the race.