Hinchcliffe grabbed the lead for good with 34 laps to go and finished 1.5 seconds ahead of Andretti Autosport teammate and defending IndyCar champion Ryan Hunter-Reay.
The result gave Andretti the two top spots at Iowa for a second consecutive year following Hunter-Reay's victory and Marco Andretti's second-place finish at Newton in 2012.
With Sunday's second-place finish, Hunter-Reay pulled to within nine points leader Helio Castroneves.
Claiming third place was Indianapolis 500 winner Tony Kanaan. Ed Carpenter and Graham Rahal rounded out the Top 5.