Mahan birdied the final three holes at the Glen Abbey Golf Club to fire an 8-under 64 for a 36-hole total of 131. John Merrick was alone in second at 133 after a tournament-low 62 and Bubba Watson was at 135 in third place.
Mahan played in the final group on Sunday at both the U.S. Open last month and the British Open last week. He wound up tied for fourth while Justin Rose was capturing the U.S. Open and he finished tied for ninth at Muirfield as Phil Mickelson was winning the British Open for the first time.
Even though Mahan has yet to win this year, he is 14th on the FedEx Cup points list and has won more than $2 million.
Patrick Reed and Aaron Baddeley shared fourth place at 136.
It took a score of 1-under 143 to make the cut and among those making it on the nose was Canadian David Hearn, who had to birdie the final three holes and convert a 47-foot putt on the 18th green to do so.
Hearn was involved in a playoff at the John Deere Classic in his most recent outing, a tournament he let slip through his hands when he missed a putt of less than five feet in the sudden death showdown eventually won by 19-year-old Jordan Spieth.
Among those missing the cut was Luke Donald, ranked ninth in the world and one of those who made the trip from Scotland to Ontario following the British Open.