Niese looked sharp early, allowing just one baserunner his first time through the order. But after Jimmy Rollins reached second base on a bloop double with two outs in the third, the left-hander gave up an RBI single to Kevin Frandsen and plunked Chase Utley, before striking out Ryan Howard to end the inning.
The Phillies kept on rallying into the fourth inning, when David Wright was unable to glove John Mayberry's leadoff infield single. The next batter, Ty Wigginton, doubled home Mayberry to tie the game at 2. The Phillies then took the lead for good in the fifth, when Frandsen hit a leadoff double, Utley moved him to second on a groundout and Howard scored him on a sacrifice fly.
The other defining moment of Niese's start came in the sixth, when the left-hander dropped a popup with a man on third base and one out. Saying he was waiting for an infielder to call him off, Niese heard the call too late and was unable to glove the ball, though a run did not score.
In essence, that sequence defined the theme of his start: damage control.
"He threw the ball fine," Mets manager Terry Collins said of Niese. "The fact that he really had to pitch hard to get out of a couple of jams wore him out a little bit."
Similar offensive execution was lacking for the Mets, who scored their only runs off starter Kyle Kendrick on early solo homers by Mike Baxter and Scott Hairston. Kendrick grew stronger as the game wore on, retiring 13 straight batters from the fourth through eighth innings and drawing a standing ovation as he left the mound.
"I feel like I've gotten a lot better with ... finding out what kind of pitcher I am and trusting that," said Kendrick, who gave up five runs to the Mets in a relief appearance earlier this year. "There are going to be days when you get hit around. That happens to everybody. But you go out there and just trust your stuff and work with what you have and know what kind of pitcher you are -- don't worry about the other things and do your business."
The Mets came into the game hoping to go 8-1 at Citizens Bank Park this season, which would have matched the eight victories they recorded in Philadelphia in 1972. The Mets went 22-5 at Veterans Stadium from 1969-71, but until this summer, had not won seven games at Philadelphia in any season since that time.
Despite the loss, the Mets are still winning the season series, 10-5, and are assured of a positive record against the Phillies for the first time since 2008.
Their biggest scare in Thursday's finale came not from the Phillies, but from pinch-hitter Justin Turner, who took a 94-mph Jonathan Papelbon fastball off his helmet in the ninth. Though Turner came out of the game, he insisted afterward that he was unaffected.
"I got up and ran to first," Turner said. "I'm fine."
So the Mets emerged from Philadelphia mostly unscathed, and even somewhat buoyant. Their quest for third place took a small hit on Thursday, but the Mets still have more than a month to achieve their remaining goals. Winning two-thirds of their games in Philadelphia was a start.
"It's always a good road trip when you come into Philly and take two of three," Niese said. "Today was tough, but we're on a positive direction right now. We're playing well."