Peter Tomasulo finished alone in third place at 12-under-par 276 after a round of 66 at Brookside Golf & Country Club. Blaine McCallister was one shot further back at 11-under-par 277 while Michael Harris took fifth place at 10-under-par 278.
Seki was two shots behind Johnson to start the final round but collected three birdies and a bogey over his first four holes to move to 13 under. Seki continued his fine play with a birdie at the par-3 eighth and added a birdie at the par-3 12th to reach minus-15.
The 24-year-old then birdied the par-3 17th on his way to his first career victory on the Canadian Tour despite a bogey at the closing hole.
'I was really nervous out there today,' said Seki. 'I hadn't been in this position very often, so I'm still learning. I really wasn't sure how I would react.'
Johnson had a strong start with back-to-back birdies from the fourth but he fell backwards with a double bogey at the par-5 seventh and a bogey at the eighth. He countered with a birdie at the 10th but gave that shot back with a bogey at the following hole.
The 32-year-old responded with a birdie at the 15th but stumbled with a bogey at the very next hole. Johnson then birdied the 17th to finish within two of Seki after a round of 72.
Brennan Webb, Tom Johnson, Chris Parra and Scott Gibson shared sixth place at 9-under-par 279. Alex Rocha was next at 8-under-par 280.