Encarnacion has hit 14 more home runs this year than he has in any other season since he joined the big leagues in 2005. He is only one behind Josh Hamilton of the Texas Rangers for most home runs in the majors.
He is the eighth player in franchise history to reach 40 homers for a season.
The big Toronto inning broke a 2-2 tie and gave the win to Henderson Alvarez (9-12), who gave up three runs on five hits over seven innings.
Adam Lind hit a two-run homer for the Blue Jays in the first, but the Mariners tied it in the second on a two-run double from Carlos Peguero.
All five runs in the fourth were scored after two were out and came off Felix Hernandez (13-8), who has lost his last three starts after winning nine straight decisions.
That brought up Encarnacion, who hit a 1-2 pitch over the wall in left-center.
Toronto avoided a sweep at the hands of the Mariners in the three-game series.