Japan, who demolished the North Americans 46-8 last Sunday in the first test in Sendai, went ahead after nine minutes thanks to a try from Go Aruga and Kensuke Hatakeyama added another on 20 minutes to help the home side take a 12-3 halftime lead.
Japan continued to dominate in the second half with Michael Leitch and substitute Ayumu Goromaru adding two more tries.
The Canadians scored on penalties in each half from James Prichard and Ander Monro.
Japan improved their overall record against the Canadians to 13 wins, 10 defeats and three draws.