Juan Francisco went 3-for-3 with a solo homer and three runs scored and Adam Lind, fresh off the 15-day disabled list, had a two-run blast and three RBI for Toronto, which outscored the Phillies 31-11 in the series.
"Realistically if you look at the way the lineup is right now, there are some pretty good hitters here," said Blue Jays manager John Gibbons. "And then of course you put us in this ballpark, it's home-run heaven."
Blue Jays starter R.A. Dickey (3-3) worked 6 1/3 innings and allowed three runs on seven hits, while fanning eight.
Phils starter A.J. Burnett (2-2) was knocked around for seven runs -- six earned -- on nine hits through six frames. Luis Garcia, who was called up before the game, worked two innings and gave up five runs -- three earned -- on four hits.
"We weren't fundamentally sound for the four games (against Toronto)," said Phillies manager Ryne Sandberg. "A lot of the fundamental things we didn't execute."
Philadelphia got on the board first in the second inning for its only lead of the game. Marlon Byrd led off with a single and advanced to second on a wild pitch before Brown stroked a double to plate Byrd. Dickey, however, set down the next three batters to strand Brown at second.
The Jays answered in the home half of the second with three runs. Encarnacion clobbered a leadoff homer, No. 200 of his career. Francisco followed up with a double and made his way to third on a wild pitch. He then scored on Lind's groundout and Colby Rasmus hit a solo shot to right.
In the third, Jose Reyes led off with a ground-rule double, which was aided by fan interference. Reyes then stole third and Bautista knocked him in with a sacrifice fly to center.
The Phillies came within 4-2 in the fifth. A leadoff walk followed by a wild pitch sent Tony Gwynn Jr. to second and Rollins ripped a single to plate Gwynn.
Toronto once again answered in the bottom half. Reyes was hit by a pitch, stole second and arrived at third on a passed ball. He then scored on a groundout by Bautista with one down.
The Jays kept rolling in the sixth on a two-run homer from Lind. Francisco walked to lead off the inning and Lind barely stroked the ball over the wall in left.
Rollins hit a one-out double and made his way to third after a wild pitch before Utley plated him with a triple. The Phils trailed 7-3 in the seventh.
In the home half of the seventh, though, Toronto tacked on three more. With two outs, Bautista singled before Encarnacion went deep again to left. Francisco made it back-to-back round trippers on the very next pitch.
Melky Cabrera hit a two-run triple in the bottom of the eighth to account for the Jays' final runs.
Freddy Galvis walked to lead off the ninth and Ben Revere singled him in before Howard's two-run bomb.