Starting the race in seventh place after being penalised in the rain-hit qualifying round on Saturday, Marquez grabbed the second position early even as Rossi produced a dominating show to emerge as the leader.
With just four laps to go, Rossi slipped at the first turn of the 16th, allowing Marquez to take control over the proceedings.
Marquez had sealed his world title in October in Japan.
Marquez, who had crashed out of the Australian GP, secured the win with a timing of 40.32.372mins, while Rossi finished 18th in the end, 58.288s behind the Spaniard.
"I was feeling good towards the end and was trying to catch Valentino but when I saw him make that unfortunate mistake, I calmed down and just finished the race," Marquez said.
Team Suzuki Ecstar's Arins finishes second, while Tech 3 Yamaha's J Zarco was third.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)