Alvarez (9-12) allowed three runs on five hits and three walks for Toronto, which won for the fifth time in seven games.
Adam Lind added a two-run homer and Brett Lawrie also knocked in a pair in the victory.
Felix Hernandez (13-8) was hammered for seven runs on 10 hits and a walk through just four innings for the Mariners, who were attempting to record their first series sweep of the Blue Jays in Toronto since May 11-13, 2001.
"The Blue Jays were hitting today," said Seattle catcher Jon Jaso. "They were swinging the bats well."
Toronto jumped out to an early lead in the bottom of the first inning with Lind's two-run homer to right field.
Colby Rasmus hit a one-out single prior to Lind's 10th home run of the year.
But the Mariners answered with a pair of runs in the second inning when Jaso worked a leadoff walk and moved to second on a Justin Smoak single before both advanced a base on Luis Jimenez's groundout and came home on a Carlos Peguero double to left field that landed just out of the reach of Rajai Davis.
The Blue Jays, though, regained the lead in the fourth inning after Jeff Mathis reached first on a bunt single and moved to third on Anthony Gose's double to right field. Lawrie followed with a base hit up the middle to plate Mathis and Gose.
Following a Rasmus walk, Encarnacion hammered a ball over the left-center field wall to give Toronto a 7-2 advantage.
"It was a good pitch, it was down," Hernandez said of his offering to Encarnacion.
Kelly Johnson hit a leadoff single in the fifth inning, stole second and third and came home on a Mathis base hit to extend the Blue Jays' lead.
Seattle got a run back in the seventh inning with Dustin Ackley's solo shot to center field, but Brad Lincoln left a runner on third in the eighth and Aaron Loup tossed a scoreless ninth to close out the game.
Encarnacion's home run was his 40th of the season, marking just the fourth time in Blue Jays history that two different players hit 40 homers in back-to- back seasons. Jose Bautista hit 43 home runs last year ... Alvarez improved to 2-0 in three career starts against the Mariners ... Hernandez fell to 3-4 in nine career starts against Toronto ... Seattle won the season series between the teams, 6-3.
09/14 02:39:42 ET