Even a heavy crash in morning practice failed to slow the Moto2 champion, who had looked unstoppable at the Texas track ever since first testing there in March.
Marquez reeled off three ever-faster laps at the start of final qualifying, eventually getting down to a 2m03.021s.
At that stage he was nearly a second clear of the pack.
It took a huge late effort from his team-mate Dani Pedrosa to get the gap down to 0.254 seconds, the elder works Honda rider finding 0.7s on his final dash.
Jorge Lorenzo had to settle for third on the fastest Yamaha. He was a full 1.3s quicker than team-mate Valentino Rossi, who could only manage eighth.
Cal Crutchlow was the best of those who had not tested at Austin as he put the Tech 3 Yamaha fourth, beating LCR Honda's Stefan Bradl - the only non-factory rider with experience of the venue.
Andrea Dovizioso was Ducati's lead runner again, claming the final second row spot.
Aleix Espargaro again produced an extraordinary performance on Aspar's CRT bike.
He made it through the first part of qualifying at prototype rider Andrea Iannone's expense, then took ninth on the final grid - ahead of Nicky Hayden, Bradley Smith and Ben Spies.
Until the last moments of Q1 it looked like it would be Smith, not Iannone, who missed the cut, but a big improvement from the young Briton got him through.
Karel Abraham will miss Sunday's race having clashed with Bryan Staring early in Q1. The Czech rider sustained a fractured collarbone.