Ducati's Andrea Dovizioso took second with Valentino Rossi, winner of the Qatar season-opener for Yamaha last month, third to keep the overall lead by a single point. Rossi’s team-mate Jorge Lorenzo, suffering from bronchitis, was fourth.
Marquez, who has won the past three races in Austin from pole as well as the past six MotoGP rounds in the United States, lost out to Dovizioso at the start but swept past the Italian on lap five.
The 22-year-old Honda rider then pulled away steadily to finish 2.354s ahead of Dovizioso, who appeared to run out of fuel on his slowdown lap after the chequered flag.
Ducati's Andrea Dovizioso took second with Italian Valentino Rossi, winner of the Qatar season-opener for Yamaha last month, third to keep the overall lead by a single point. Spanish team mate Jorge Lorenzo was fourth.
There was immediate drama on the opening lap when Britain's Scott Redding, who had qualified an impressive sixth, fell and took Spaniard Pol Espargaro with him.
Rossi now has 41 points to Dovizioso's 40 with two times champion Marquez, who started the season with only a fifth place after having to climb back from last at the first corner, on 36.
"We recovered some points...but we need to work really hard in the next races," said Marquez. "I felt really good at the beginning, I tried to save some tyres, then I pushed some laps and managed the distance."
The scheduled race start was delayed by 35 minutes as track workers dried the track after a water spillage, due to overnight rain, from an overhead footbridge at Turn 3.
POINTS AFTER TWO OF 19 ROUNDS
Speed Up Racing's Sam Lowes of Britain shook off the effects of big crashes in practice and qualifying to win his first race at the level.
Lowes overtook Ajo Motorsport's Johann Zarco to lead with six laps to go. As Zarco and Xavier Simeon tried to reel him back in, they made contact, with the latter crashing.
Zarco recovered to finish second ahead of rookie Alex Rins on the Paginas Amarillas HP40 Kalex.
British Honda rider Danny Kent took his first win of 2015 and the third of his career.
Kent, 21, started from pole and held off 15-year-old French sensation Fabio Quartararo, who was making just his second start at this level. Spain's Efren Vazquez was third.
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Original source: Marquez roars back at Austin MotoGP