Andretti Autosport's Hunter-Reay grabbed the lead on lap 57 following a round of pit stops and held on the rest of the way through the 1.75-mile, 11-turn Exhibition Place street course in Toronto.
Hunter-Reay's win also vaulted him into the IndyCar points lead, giving him a 34-point cushion over Will Power, who finished 15th after sustaining a broken wing on his left-front tire.
Charlie Kimball logged a career-best second-place finish at Toronto, while Mike Conway, Tony Kanaan and Oriol Servia completed the Top 5.
Millions of Getty images now available for free via embed tool
Boston schools pull out free condoms over wrapping complaints