The win allowed Marquez to widen the gap with Italian rider Andrea Dovizioso, who came second at the MotorLand Aragon circuit, to 98 points, Efe reports.
Marquez now has a good chance to secure his sixth world title in the upcoming Thai Grand Prix.
Kicking off the race from pole position, Marquez had a good start, followed by Frenchman Fabio Quartararo, Australia's Jack Miller (Ducati Desmosedici GP19) and Spaniards Maverick Vinales and Aleix Espargaro (Aprilia RS-GP).
The action started in the first lap, as Spaniard Alex Rins' Suzuki GSX RR hit the rear part of Franco Morbidelli's Yamaha YZR M 1, resulting in the Italian being out of the race.
The MotoGP Race Direction opened an investigation into the accident and decided to hand the Spaniard a long-lap penalty.
Rins served the sanction in the seventh lap, but he barely conceded 2.4 seconds, which allowed him to maintain his 12th spot.
As the opening lap was over, Marquez was leading his closest chasers Jack Miller of Australia by a second and the gap was widening with every lap.
Such was the increasing gap that Marquez put the race out of his rivals' reach just five laps into the race.
Behind him, a three-way battle was taking place between Miller, Quartararo and Spaniard Maverick Vinales for a second place alongside the dominant Marquez on the podium.
Ultimately the real battle of the race came down to a duel between Miller and Vinales with Quartararo, Dovizioso and Espargaro chasing them.
Dovizioso dug deep, coming back from 10th place to claim the second spot with only two laps to go, with neither Vinales nor Miller being able to hold him off.
It was the Italian racer who finished second, while Miller completed the podium.
( With inputs from IANS )