With a speedy runner on first and two outs in the 10th, Werth made a sensational grab of David Wright's sinking liner in the right-center gap.
If the ball gets by him, Fernando Martinez probably scores the winning run. But rather than play it safe and glove the ball on a hop, Werth went all out.
"It was just one of those deals where I thought it was worth it," he said. "When the ball came out of the lights I thought, ohh, it's much closer than I expected. When I dove for it, I didn't expect to catch it."
Somehow he did, and then Utley led off the 11th with his 15th home run.
His third homer in two nights that nestled into the right-field corner at spacious Citi Field came on the second pitch from Bobby Parnell (2-1), handing the hard-throwing rookie his first big league loss.
It's the only home run Parnell has allowed in 29 career innings.
"Fastball in. The pitch he was looking for," Parnell said. "He's a good hitter. That's the pitch he wanted and that's what he wanted to do with it."
Utley had a testy exchange earlier in the game with Mets starter Mike Pelfrey, who got annoyed when the slugger stepped out of the box.
"I was ready to make a pitch and he called timeout," Pelfrey said. "I got upset and told him to get in the box. I don't even know the guy. I was just trying to compete and execute a pitch.
"I got caught up in the moment. I probably shouldn't have said anything."
Utley downplayed the whole thing.
"It seemed like he got a little frustrated. I wasn't trying to frustrate him. I was just trying to have a good at-bat," Utley said.
New York built a three-run lead against World Series MVP Cole Hamels, who faced the Mets for the first time since calling them "choke artists" in the offseason -- the latest in a series of verbal barbs between the NL East rivals.
But the Phillies rallied to tie it 4-all in the seventh against Pelfrey and the New York bullpen. The Mets have lost six times this season after leading by at least three runs.
The Mets stranded a season-high 16 runners, eight from innings seven through 10. Still, they nearly won it in the 10th on Wright's liner.
"If he hadn't of caught it, the guy would have scored," Phillies manager Charlie Manuel said.
Wright, who had three hits and two stolen bases, yanked off his helmet in frustration at first base after Werth's diving catch. Wright also made a key error in the seventh.
Jimmy Rollins went 0 for 5 with an RBI for the Phillies in his return to the leadoff spot after two games batting sixth. Philadelphia is 6-3 on a 10-game trip, improving to a major league-best 22-9 away from home.
New York dropped to 18-10 at Citi Field with only its fourth loss in 16 home games. The Mets are 4-2 against Philadelphia this season, but they trail the first-place Phillies by three games.
It was Philadelphia's first win in four games at New York's new home.
"Every game we play with them is big. It's a rivalry. Everything about it is good," Manuel said. "We like to play them and they like to play us. We're pretty even teams."
Coming off a five-hit shutout of the Los Angeles Dodgers, Hamels allowed four runs in five innings. He gave up 11 hits, matching a career high.
"I have better things to worry about in my life than to worry about Cole Hamels and what he said," Mets outfielder Carlos Beltran said.
Pelfrey doubled off the base of the left-field fence and scored in the third, then had a bloop RBI single in a three-run fourth. ... Utley has 17 career multihomer games, including two this season.