Marquez led all seven MotoGP on-track sessions during the weekend - four practices, qualifying, the warm-up and the race.
"I think we did the best we can in MotoGP," Marquez said. "I feel so good this weekend."
Marquez started from the pole but slipped to third at the start of the 27-lap race. But after running in a tight lead pack with leader Jorge Lorenzo and teammate Dani Pedrosa, Marquez passed Pedrosa for second on Lap 9. He then began to stalk the Yamaha of reigning World Champion Lorenzo.
Marquez made his decisive move on Lap 13, diving under Lorenzo for the lead in Turn 2. Lorenzo stayed within one second of Marquez for the next five laps before Marquez pulled away.
Two-time Red Bull Indianapolis GP winner Pedrosa rallied to pass Lorenzo for second on Lap 25 and ended up 3.495 seconds behind Marquez at the finish. Lorenzo completed the podium finishers in third.
Marquez completed a sweep of all three MotoGP races this season in America and also has won his last five starts in the United States. He won the Moto2 races in 2011 and 2012 at Indianapolis.
"Yeah, this will be my second country," Marquez said.
Marquez expanded his lead over Pedrosa in the MotoGP World Championship standings to 21 points with the victory. Marquez is trying to become the first rookie to win the premier-class world title since Roberts in 1978.
2006 World Champion Nicky Hayden led the American contingent, finishing ninth on his Ducati Team machine. Hayden and teammate Andrea Dovizioso collided and hopped the curb exiting the final turn on the final lap, opening the door for Bradley Smith's Yamaha to pass both of them for eighth.
American Colin Edwards finished 13th on his NGM Mobile Forward Racing FTR-Kawasaki, while American wild-card Blake Young crashed out on Lap 1 on his Attack Performance Racing APR.
Spanish riders also won the Moto2 and Moto3 races.
Esteve Rabat passed Takaaki Nakagami on Lap 23 of the 25-lap Moto2 race to win by .766 of a second on his Tuenti HP 40 Kalex. Alex Rins prevailed in a Moto3 race that featured numerous lead changes over 23 laps, holding off teammate Alex Marquez - the younger brother of MotoGP race winner Marc Marquez - by .177 of a second on his Estrella Galicia 0,0 KTM.
Malaysian rider Hafizh Syahrin won the second AMA Pro Vance & Hines Harley-Davidson Series race by .060 of a second over Steve Rapp. Shane Turpin won the FIM eRoadRacing World Cup race for electric motorcycles by 13.733 seconds over Icon Brammo teammate Eric Bostrom.
-- From Indianapolis Motor Speedway Public Relations