Marquez's win came despite starting in seventh position after being hit with a grid penalty, surging past nine-time world champion Valentino Rossi who crashed out when leading.
World champion Marc Marquez won his ninth race of the MotoGP season after Italian great Valentino Rossi crashed out four laps from the finish while leading the Malaysian Grand Prix on Sunday.
Marquez wrapped up his fifth world title with three races to spare in Japan last month but looked like having to settle for second in front of nearly 104,000 fans at the Sepang International Circuit.
Seven-times world champion Rossi, who last won 26 races in Assen, had streaked past pole-sitter Johann Zarco at the start and built up a lead of seven tenths of a second when his bike came out from under him on turn one.
Marquez's 44th win so far
Marquez, who had topped the times in qualifying but relegated six places on the grid for impeding Suzuki's Andrea Iannone, safely negotiated the remaining four laps to secure his 44th win in the top class of grand prix racing.
The Spaniard's victory in 40 minutes 32.372 seconds also secured the constructors' championship for Honda for the fourth straight year with one round of the season remaining.
"I was pushing hard and starting to catch Vale but when I saw his mistake then I cooled down and just finished the race," said Marquez.
"It was the best way to celebrate the championship ..."
Alex Rins finished second for Suzuki ahead of Yamaha rider Zarco with Rossi's team mate Maverick Vinales, who gave Yamaha a first win of the season in Australia last week, a creditable fourth after starting 11th on the grid.
Italian Andrea Dovizioso was sixth behind Honda's Dani Pedrosa to ensure he will finish second in the championship ahead of Rossi, who crossed the line in 18th.
Hafizh Syahrin, who became the first Malaysian rider to compete in MotoGP this season, finished 10th on his Yamaha despite starting at the back of the grid.
Earlier, both junior titles were decided with Italian Pecco Bagnaia sealing the Moto2 world championship for the Sky Racing VR46 team by finishing third as his team mate Luca Marini, team owner Rossi's half-brother, secured a maiden victory.
Spain's Jorge Martin secured the Moto3 title with his seventh win of a season he has dominated for Honda.