Simon Pagenaud finished seventh and increased his lead over Will Power to 43 points standings with one race remaining in the season. Pagenaud was running fifth with 10 laps left, but had to back off to save fuel in the closing laps.
Power crashed just past the midpoint of the race and finished 20th. He was not permitted to return to the race because of concussion symptoms.
The two Penske drivers are the only ones still in contention for the title.
It was the first IndyCar race at The Glen since Power won from the pole in 2010.Dixon won the pole Saturday with a speed of over 147 mph and a record-shattering time that eclipsed the previous record by nearly six seconds on the track's new pavement.
In Sunday morning's 30-minute warmup, Dixon practiced his starts and nearly lost it once.
Once the green flag dropped, he was flawless, consistently opening big leads and saving enough fuel over the final laps to win by 16.5 seconds. Dixon announced after the race on pit road that he was donating his winnings to the family of the late Justin Wilson, who died last August after being struck in the head by debris from a crash in an IndyCar race at Pocono Raceway.
Power's drive toward the championship suffered a damaging blow when his No. 12 Team Penske Chevy made contact with Charlie Kimball on lap 39 coming out of the high-speed esses.
Kimball hit the left rear tire of Power's No. 12 in the narrow section of the track at the top of the hill. He got a huge run on the outside and made contact, sending Power hard into the barrier and bringing out a caution as debris scattered all over the track.