The Phillies had several opportunities but wound up stranding four runners in scoring position in the first three innings alone. They wasted another great chance in the fifth inning, but homered in the ninth before leaving the potential tying run standing on second base.
Chase Utley came up with the biggest hit of the game, a two-run homer in the ninth inning that accounted for the final margin. Utley took Mets closer Bobby Parnell to the second deck in right field to pull the Phillies within one run, but they couldn't complete the comeback.
"That's what good teams do. We're working toward that," said All-Star Domonic Brown, the man standing on second when the game ended. "Chase had a big home run there. I'm just trying to do my little part, whatever that is. I got lucky and got a pitch up to drive."
Brown doubled to left-center in the ninth inning, but the game ended on a sharply hit ball to second base by Darin Ruf. That was just one of a few missed opportunities for the Phillies, who couldn't convert a bases-loaded opportunity in the fifth inning when trailing by one run.
That may have been Philadelphia's best chance to assert control. Hamels began that rally with a single, and the Phillies loaded the bases on a single and a walk. Utley made it a 3-2 game with a sacrifice fly, and that brought Brown to the plate with two men on base.
Mets starter Zack Wheeler fell behind, 3-0, against Brown, and manager Charlie Manuel gave his top run producer the discretion to swing. Brown wound up flying out on the next pitch, and after Wheeler walked Ruf, reliever Gonzalez Germen entered to strike out Delmon Young with the bases loaded.
"I don't know if it was [a ball], but it definitely wasn't a pitch I wanted to swing at," said Brown of that key fifth-inning at-bat. "I've got a man in scoring position, and I was trying to drive the ball in [at] 3-0. I was trying to get a pitch up to drive. It's that simple, but it's not that easy. I'm looking for a pitch middle-in. He threw it away and I was trying to take, but by that time the swing was already through."
Manuel said after the game that he routinely allows Brown to swing in 3-0 counts with runners on base. The strategy didn't work this time, but Manuel trusts Brown to make the right decision.
"He's got 70 RBIs and 24 homers," Manuel said of his cleanup man. "I feel like right now he's our guy that knocks the runs in. ... I think the ball was up a little bit, and he skied it in the air to left-center."
Southpaw Hamels (4-12) went into this game on a hot streak. The 29-year-old had completed at least seven innings and allowed two earned runs or fewer in each of his last three starts before the All-Star break, but he had trouble finding the strike zone on Saturday.
Hamels walked two batters in the first inning and frequently wiped his hands, and he said afterward that the heat affected his grip. Marlon Byrd and Juan Lagares came through with run-scoring hits in the first inning, and the Phillies left the inning trailing, 3-1.
"You can't always go out with your best stuff, but you have to make adjustments," said Hamels. "I wasn't able to make the adjustments as quickly as I would have liked in that first inning. I made the adjustments once the game went on, but the first inning was obviously what decided the whole game."
Jimmy Rollins got the Phillies (49-49) started with a leadoff home run in the first inning, the 45th time in his career he's led off a game by going deep. But perhaps more important, the long drive was the first homer for Rollins in 161 at-bats, the fifth-longest drought of his career.
The Phillies, who have yet to push two games over .500 all season, allowed the game to get away on a couple of insurance runs. David Wright singled in a key run in the fifth inning, and Daniel Murphy singled home another run in the seventh. Eight of the Mets' 10 hits went for singles.
Rookie Germen earned his first career win for the Mets (42-51).
Philadelphia scored 13 runs in Friday's series opener, and Manuel wishes the team could have saved some of that offense.
"Yesterday our right-handed hitters could hit those balls to right field and get hits. Today we couldn't do it," said Manuel. "It felt like we got anxious on [Wheeler's] fastball up. He was throwing some fastballs up, and we were definitely chasing them out of the zone. I said before the game that we had to make sure he got the ball down in the strike zone. We had chances, but we didn't get it done."
The loss snapped the Phillies' streak of seven wins at Citi Field, but they maintain a 7-4 edge over the Mets this season. Sunday's series finale will pit All-Star Cliff Lee against Matt Harvey, who started the All-Star Game for the National League.
"We've got a guy pretty good, too. That's what makes it great," said Manuel of the matchup. "That's what makes it a good game. How do we have to approach him? We've got to make him throw strikes and try to get good balls to hit. He's a power pitcher with overpowering stuff, and his secondary stuff is real good. He commands it. He's tough to beat, but that doesn't mean we can't do it."