Heffernan completed his second tour title with a tournament-record score of 20-under-par 268. The previous record of 269 was set last year by Matt Hansen, Erik Compton, John Mallinger, and Jeff Quinney.
John Ellis shared second place for the second straight week. He and Joseph Lanza each closed with 5-under 67s to tie for second at minus-19.
Adam Speirs, who with Heffernan comprised the all-Canadian final pairing, posted a 2-under 70 at Brookside Country Club. Speirs ended alongside Stephen Gangluff and Spencer Levin at 18-under-par 270.
That final pairing was the first All-Canadian final twosome since the 2003 MTS Classic.
Heffernan collected two birdies and seven pars on the front nine to turn at 17 under. He drained back-to-back birdies from the 14th, then rolled in a 4-footer for birdie at the last for the win.
'I was chasing pretty well all day long,' said Heffernan, who trailed several players during the final round. 'This was my nemesis course, but it worked out well this time.'
The win for Heffernan, a Calgary native, means three of the last five winners on the Canadian Tour have been Canadians.
Eugene Smith ended alone in seventh at 17-under-par 271 after a closing 68. Matt Bettencourt and Bret Guetz shared eighth at minus-16.