Title rival Pol Espargaro, on pole in the previous three consecutive races, was in contention but with five minutes to go dropped the front of his Pons Kalex at Turn 15.
The Spaniard did at least have the comfort of watching the rest of the field fail to beat his benchmark, allowing him to hang on to second.
In his absence however no one was seriously able to challenge Marquez in the final minutes. The Monlau Suter rider currently leads the championship by 48 points heading into the final six races.
With Espargaro unable to improve and Marquez not needing to, the final minutes centred around the battle for third, eventually decided in favour of Marc VDS's Scott Redding.
Takaaki Nakagami and Andrea Iannone were also in the mix, but eventually had to settle for fourth and fifth respectively.
It is only the second time all year Nakagami (Italtrans Kalex) has cracked the top four.
Iannone, set to step up into Ducati's satellite MotoGP team in 2013, finished just over one quarter of a second down on Marquez.
Sixth went to Thomas Luthi (Paddock Suter), who narrowly edged out Esteve Rabat (Pons Kalex), Ratthapark Wilairot (Gresini Suter) and Mika Kallio (Marc VDS Kalex).