Michael Saunders and Devon Travis also homered for the Jays, whose five home runs were a season high as were their 13 runs and 17 hits.
Josh Donaldson went 3-for-3, reached base five times and scored three runs for Toronto, which outscored the Phillies 31-7 in winning the last three contests of a four-game home-and-home series.
The Blue Jays also won for the sixth time in seven games, and improved to 19-8 in their last 27.
Philadelphia lost for the 20th time in its last 26 games.
Pillar, who hit a leadoff homer off reliever Andrew Bailey in the seventh and a two-run shot off David Hernandez in the eighth, increased his season total to seven. It was the second multi-homer of his career. The other came June 2, 2015 against Washington.
Encarnacion, 2-for-4 in the game, homered for the sixth time in as many games and his 12th time in 20 career contests at Citizens Bank Park. He also increased his major league-leading RBI total to 61.
Former Phillie J.A. Happ (8-3) went seven innings to earn the victory, allowing an unearned run and three hits while striking out five and walking two. He improved to 4-0 in his career against his former team.
Philadelphia starter Aaron Nola (5-6) lasted three innings, the shortest outing of his career. Nola, whose 3 2/3-inning appearance against Washington in his previous start had been his briefest, allowed eight runs (six earned) and eight hits while striking out five and walking three.
Encarnacion started the onslaught with a two-run homer in the first inning, hitting Nola's 1-1 curveball into the seats in left field after Donaldson singled. It was Encarnacion's 18th homer of the season.
Saunders followed with his 12th homer of the season, the fifth time this season the Jays have hit back-to-back home runs. Encarnacion and Saunders did it five days earlier against Baltimore.
Russell Martin made it 4-0 with an RBI single in the third and Toronto chased Nola by scoring four times in the fourth.
Encarnacion had the key blow in the fourth with a two-run single off reliever Colton Murray. Jose Bautista also brought in a run with a single and another came home when Phillies left fielder Tyler Goeddel dropped Martin's fly ball.
Pillar's leadoff homer in the seventh made it 9-0.
After Jimmy Paredes drove in a Phillies run with a seventh-inning grounder, the Jays tacked on four runs in the eighth against Hernandez. Travis led off the inning with his second homer of the season.
The Jays also picked up a run on Martin's double. He drove in Encarnacion, who was on first when Saunders flew out to Philadelphia center fielder Odubel Herrera for the inning's second out. Herrera, thinking the inning was over, threw the ball into the stands for an error, allowing Encarnacion to advance to third. Pillar followed with a two-run homer.
Herrera's RBI single in the eighth made it 13-2.
NOTES: Blue Jays RF Jose Bautista left the game in the seventh inning with a sore left big toe. He is scheduled to undergo precautionary X-rays, but is listed as day-to-day. ... Philadelphia RHP Alec Asher, who is on the disabled list at Triple-A Lehigh Valley, was suspended 80 games for violating Major League Baseball's drug agreement after a positive test for dehydrochlormethyltestosterone, an anabolic steroid used to increase speed and strength. It is the same substance that resulted in an 80-game suspension for Phillies LHP Daniel Stumpf in April. ... Toronto LF Michael Saunders returned to the starting lineup. He was removed from Tuesday's victory over Philadelphia with a sore thigh and then introduced as a pinch hitter in Wednesday's game against the Phillies but removed in favor of INF Andy Burns.