Marquez shot out of the blocks and beat his brother Alex, the pole-sitter, into the opening turn. Alex Marquez was able to quickly regain the lead but ran wide a turn later to hand it back, and his brother made no mistakes from that point on to claim the chequered flag
.Victory moved seven-times MotoGP champion Marquez up to 399 points in the championship standings, 44 ahead of Martin, who did not compete after suffering a wrist fracture.
If Marquez is able to extend his lead to 74 points at next week's Qatar Grand Prix, he can seal an eighth championship title with two rounds remaining in the season.
"We did a perfect race, so I'm super, super happy," said Marquez, who won the race by a commanding margin of over four seconds.
"But my mentality still cannot change. I have to keep focus, keep pushing. There are not many races to go, but there are many moments left. So, we must be super confident."
Saturday's sprint winner Pedro Acosta of KTM finished second, while Gresini's Alex was third.
After losing the lead to his brother, Alex Marquez was drawn into a duel with Acosta, who stuck to the wheel of the Gresini rider for several laps before expertly overtaking him at the midway point of the race.
By then, however, the distance to the leader had already grown too large to overcome.
Aprilia rider Marco Bezzecchi, an outside contender for the title, finished in sixth place after being overtaken late by both Trackhouse rider Ai Ogura and Tech3's Enea Bastianini.
Martin absent
Marquez's main title rival Martin had initially looked set to return in Malaysia and briefly attempted to compete in Saturday morning's practice session.
However, the Aprilia rider was visibly struggling and eventually did not take part in qualifying, ending his weekend to continue his recovery from the fracture he sustained in the crash at Phillip Island last week.
The Spaniard, who won the title in 2024, conceded that his MotoGP title challenge was effectively over after his withdrawal.
The MotoGP season next moves to the Lusail International Circuit for the Qatar Grand Prix, which is set to go ahead next week despite pushback from riders concerned about going there during the war against Iran.