Romero (5-3) allowed two hits, walked one and struck out seven.
Jeremy Accardo worked a perfect eighth and Dirk Hayhurst finished the three-hitter, allowing Werth's sacrifice fly in the ninth.
Toronto won for the fourth time in five games and has beaten the Phillies in six straight. The Blue Jays swept a three-game series in Philadelphia last week. After that, the Phillies were swept by Baltimore and lost two of three in a World Series rematch at Tampa Bay.
"We're not really playing what you'd call 'together baseball' right now," Phillies manager Charlie Manuel said before the game. Toronto opened the scoring in the second when Scott Rolen doubled and came around on a single by Alex Rios, who snapped an 0-for-12 skid. Rolen's double extended his hitting streak to a career-high 15 games. He's batting .429 (27 for 63) over that span.
The Blue Jays added three more in the third against left-hander Cole Hamels (4-4), who is winless in four starts. Hill hit a two-run double, stole third and scored on Rolen's sacrifice fly.
Hamels was replaced by right-hander Chan Ho Park after infield singles by Adam Lind and Kevin Millar, then was ejected by home plate umpire Mark Carlson for arguing balls and strikes as he left the field.
With Manuel and the rest of the Phillies infield at the mound, Carlson walked out to break up the conference and Manuel signaled to the bullpen. Hamels began arguing with Carlson as he walked alone to the dugout and was tossed just after crossing the foul line. He's the first Philadelphia player to be ejected this season.
Park got out of the jam but was injured when Rios hit a bouncer off the pitcher's right knee. Park picked up the loose ball and made the throw to first before falling to the ground in pain. Righty Tyler Walker replaced Park in the sixth.
Toronto lost catcher Rod Barajas in the second when he injured his right hamstring running to first on a single. Raul Chavez replaced Barajas and later hit an RBI single off Brad Lidge in the eighth. One batter late, Marco Scutaro made it 6-0 with a bases-loaded walk off J.C. Romero.
Phillies shortstop Jimmy Rollins, who is stuck in an 0 for 19 slump, sat out his second straight game.
NOTES: Hamels changed places with Saturday's starter, lefty J.A. Happ, so that he could get one more start before the All-Star break. ... Phillies LHP Antonio Bastardo will return to Philadelphia and see a doctor Monday after leaving Thursday's start in the fourth because of a shoulder strain. ... After throwing a bullpen session, Toronto RHP Roy Halladay (groin) declared himself ready to come off the 15-day DL and start Monday against Tampa Bay.
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