The Spaniard, who has also won at the track for the past three years, was chased hard for his 60th career pole in all categories by compatriot and reigning world champion Jorge Lorenzo, on a Yamaha.
Marquez, a double MotoGP champion, lapped the Circuit of the Americas with a best time of two minutes 03.188 seconds with Lorenzo 0.069 slower.
Lorenzo's Italian team mate Valentino Rossi completed the front row of the starting grid for the third race of the season.
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Marquez leads the championship with 41 points to Rossi's 33.
Italian Andrea Iannone qualified fourth for Ducati but has a three-place grid drop after causing a last-corner collision with team mate Andrea Dovizioso in Argentina last weekend.
That means Suzuki's Maverick Vinales will line up fourth with Britain's Cal Crutchlow on the LCR Honda and Dovizioso completing the second row.
(Reporting by Alan Baldwin, editing by Tony Jimenez)
