Canada finish without a win in the tournament with the title to be decided on Saturday when unbeaten Japan and the United States clash, with Fiji and Samoa playing off for third and fourth.
It was a disappointing start for Tonga in a tournament designed as a World Cup build up, with losses to Samoa and Japan before they out-gunned Canada by five tries to four on a firm Churchill Park.
With their bigger pack and an ability to control the tempo of the game, Tonga were in charge for the first 65 minutes before Canada spent the closing stages camped on the Tongan line and were rewarded with two late tries.
For both sides the tournament exposed areas to build on before the World Cup which starts next month in Japan.
"There's a lot we can learn from this," Tonga captain Siale Piutau said as he reflected on his side losing steam as the match wore on.
"We've got to get fitter and get stronger so we can compete with the Tier One nations."
Canada captain Tyler Ardron saw positives in having their tries scored by wings, but defence let them down.
"A few tackles slipped off and that's probably the difference in the end, so pretty disappointing," he said.
"We've finished some games quite well lately but the first half hasn't been the way we wanted it and we definitely have to work on that before we get to the World Cup."
With the powerful Tonga pack controlling the collision area they were able to grind their way upfield before capitalising on the flair of their backs in th first half.
They raced to a 19-3 lead with tries to fullback David Halaifonua, wing Viliami Loloea and centre Malietoa Hingano before Jeff Hassler scored for Canada just before the break.
Replacement prop Latu Talakai rumbled over with his first touch of the ball just after the resumption to extend the score to 26-8.
Sione Vailanu also scored for Tonga in the second half with Sonatane Takulua landing four of his five conversion attempts.
Patrick Parfrey and DTH van der Merwe scored second-half tries for Canada along with a late second touchdown for Hassler while fly-half Gord McRorie's only successful shot at goal was a first half penalty.