Encarnacion, who played the last six seasons with Toronto before signing a three-year, $60 million contract with Cleveland in January, hit a leadoff home run in the second, broke a 3-all tie in the fifth with a two-run double and added an RBI single in the seventh.
Encarnacion was 3 for 4 with a walk and nearly added to his total later in the seventh, but center fielder Kevin Pillar tracked down his fly ball on the warning track with two runners on.
Abraham Almonte hit a three-run homer and rookie Bradley Zimmer added a two-run single in the seventh as the Indians won for just the second time in eight games.
Trevor Bauer (8-8) allowed three runs in five innings. The right-hander lasted only 2/3 of an inning — matching the shortest start of his career — against Oakland on Sunday.
Marco Estrada (4-7) gave up five runs in 4 2/3 innings and hasn’t won since May 27.
Jose Morales, Ryan Goins and Justin Smoak drove in runs for Toronto, which took a 3-1 lead into the fifth before Cleveland scored four times.
Almonte led off with a triple and Roberto Perez walked. Erik Gonzalez’s single cut the lead to 3-2 and Francisco Lindor drew a one-out walk to load the bases. Michael Brantley’s RBI fielder’s choice tied the game.
Brantley stole second and Encarnacion lined a 3-2 pitch to the gap in left-center giving Cleveland the lead.
Encarnacion has hit 20 home runs in six consecutive seasons and has homered against all 30 major league teams.
Indians manager Terry Francona returned to the dugout at Progressive Field for the first time since June 29. He missed the home stand before the All-Star break after undergoing a heart procedure.
Blue Jays: RHP Aaron Sanchez will see a hand specialist for his recurring blister problem. He was removed from his last start after four innings because of a small blister on the middle finger of his right hand.
Indians: LHP Boone Logan (torn back muscle) will miss significant time after being injured Thursday. He was placed on the 10-day disabled list Friday.
Blue Jays: RHP Marcus Stroman (9-5) seeks his 10th win of the season Saturday. He pitched six shutout innings and defeated the Indians on May 8.
Indians: RHP Danny Salazar (3-5) will pitch the first time since June 3. He lost to the Blue Jays on May 10, allowing five runs in 2 2/3 innings.
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