While the foundations were laid on the opening lap, when he charged through from 33rd to 11th in 14 turns, he still had a massive amount of work to do in the closing stages in order to close down a nine-second gap to runaway leader Julian Simon.
Marquez simply tore the advantage apart, gaining around one second per lap. With two laps to run he moved into the lead for the first time, and while Simon attempted a fightback, Marquez eased away on the final tour to claim his ninth win of the season by just over 1.2s.
It was also his last Moto2 race before he steps up into the premier class with Honda for 2013.
Simon finished second, having looked assured of a first Moto2 victory following his own superb ride at the front of the field.
Third meanwhile went to early leader Nico Terol, whose pace in the opening laps allowed him to break away from all but Simon and oaved the way for a maiden Moto2 podium.
Thomas Luthi held off Dominique Aegerter for fourth, a battle that had also included Marquez and Gino Rea in the early stages.
Rea had been able to stay with and even move ahead of Marquez early on, having constructed his own fight from 20th on the grid, but with 12 laps to run he lost the front of his bike at the final turn trying to stay with the Spaniard.
Marquez and Aegerter had touched the lap before while braking for Turn 1, an incident for which Marquez immediately apologised.
Aegerter was the final significant obstacle Marquez faced: once past, he simply stormed away in a relentless and ultimately successful pursuit of victory.
Jordi Torres took a relatively quiet sixth ahead of Mika Kallio and Pol Espargaro, who triumphed in a seven-way fight for eighth.
The Spaniard, who finishes runner-up to Marquez in the championship, had earlier fallen while running fourth, and then fought his way back from 18th.
Andrea Iannone was also part of that fight and while he could only manage 11th he did enough to hang on to third in the championship, finishing three points ahead of Luthi.