The championship leader had already set the pace in all four practice sessions and he wasted no time in taking command of qualifying as well.
He began with a 1m38.440s, then improved on that by just 0.001 seconds on his next flying lap.
There was plenty more to come on his final set of tyres too, as Marquez blasted to a 1m37.958s.
No one could get within half a second of that pace. World champion Jorge Lorenzo managed best, putting his Yamaha second on the grid.
Tech 3's Cal Crutchlow had looked set to make it two Yamahas on the front row, only for Marquez's Honda team-mate Dani Pedrosa to demote the Briton to fourth with a late lap.
Alvaro Bautista and top home rider Nicky Hayden complete row two.
Stefan Bradl had been among the pacesetters through practice but crashed in both the pre-qualifying practice session and Q2. That left him behind Bradley Smith in eighth.
Valentino Rossi was never a factor in the pole fight. He qualified 1.3s off the pace in ninth.
Colin Edwards produced an outstanding performance to go fastest in Q1 on home ground on his CRT Forward FTR-Kawasaki.
That took him into Q2 for the first time, and he will line up on row four behind the Ducatis of Andrea Dovizioso and fellow Q1 qualifier Andrea Iannone.
Iannone's Pramac team-mate Ben Spies will miss the race after dislocating his shoulder in practice three.
Aleix Espargaro harmed his chances with a crash in the pre-qualifying practice session that left him with badly bruised hands. He could not make it out of Q1 and will start 13th.