Hunter-Reay -- who triumphed last week at the Milwaukee Mile -- took the checkered flag while under caution after the No. 6 car driven by Katherine Legge made contact with the barrier on the second-to-last lap.
Andretti Autosport's Hunter-Reay finished 1.2887 seconds ahead of his teammate and used the victory to move into second place in the IndyCar standings, three behind Will Power.
Power crashed out on the 67th lap Saturday after making contact with E.J. Viso.
A thunderstorm delayed the start of the race by 40 minutes.