Encarnacion isn't just feasting on Red Sox pitching. The first baseman homered twice for the fourth time in 13 games. He has 11 homers in his last 15 games, including five in the last three.
Xander Bogaerts and A.J. Pierzynski each had three hits and Shane Victorino belted a solo homer for the Red Sox, who have lost six straight games for the first time since ending the 2012 season on an eight-game slide.
Blue Jays right-hander Drew Hutchison (3-3) allowed just one run on six hits and two walks in 5 2/3 innings, striking out four.
Hutchison was coming off his first major-league shutout last Friday, a three- hit gem against Texas to outduel Yu Darvish and snap a seven-start personal winless streak.
Red Sox righty Clay Buchholz (2-4) gave up five runs -- four earned -- on nine hits and two walks in just 4 2/3 innings. He is 0-2 in last three starts.
Encarnacion knocked a 91 mph fastball into the first row of seats on top of the Green Monster in left field leading off the second inning. Reyes added an RBI single later in the frame for a 2-0 Blue Jays lead.
After Lind led off the third inning with a triple, Encarnacion homered on Buchholz's 1-0 curveball, sending it a row deeper into the Monster seats for a 4-0 lead.
"Uncharacteristic for what we know of Clay is that mistakes found themselves over the plate," said Red Sox manager John Farrell.
Victorino hit his first homer of the season to left field with two outs in the fourth inning for Boston's first run.
Navarro's RBI single in the fifth inning gave the Blue Jays a 5-1 lead and chased Buchholz from the game.
Aaron Loup replaced Hutchison with two runners on and two outs in the sixth inning and walked Brock Holt to load the bases, but struck out Grady Sizemore to escape.
Chris Capuano, who relieved Buchholz in the fifth, remained in the game until giving up a two-out RBI single to Anthony Gose in the seventh that gave the Blue Jays a 6-1 lead.
Mike Carp's RBI double in the eighth inning scored Victorino from first base and Bogaerts hit a double off the top of the Green Monster to plate Carp, drawing the Red Sox within 6-3 and chasing Esmil Rogers from the game.
Holt followed with an RBI single off Brett Cecil to make it a two-run game and Pierzynski's two-out single in the ninth brought the tying run to the plate, but Casey Janssen got Victorino on a game-ending groundout to secure the win and his fifth save.