Andretti Autosport member Hunter-Reay gave his boss the victory after the IndyCar legend had saved the Milwaukee event from being canceled in February by stepping in as the promoter.
Hunter-Reay finished 5.1 seconds ahead of Tony Kanaan, claiming his sixth career IndyCar victory.
Andretti said Saturday the race at the Wisconsin State Fairgrounds would return in 2013.
Andretti team member James Hinchcliffe finished third, followed by Oriol Servia and E.J. Viso.
Will Power retained his series points lead despite a 12th-place finish, maintaining a 31-point cushion over the second-place Hinchcliffe.