Recently recalled right-hander Phillippe Aumont was saddled with the loss, but Philadelphia still had its opportunities to come out on top -- most notably in the seventh.
In that frame, the Phillies had a chance to put starter Cole Hamels in line for the victory. Cesar Hernandez, after a bunt single, was advanced to second on a sacrifice bunt by Reid Brignac.
Phillies manager Ryne Sandberg then pulled back Hamels, who had thrown 125 pitches, and pinch-hit Domonic Brown. Brown entered the game hitting .314 with runners in scoring position, and had eight hits in his last 20 at-bats with RISP (.400).
It was a no-brainer move for Sandberg that paid off initially, as Brown laced a single to the opposite field.
But then Brown made what he thought was a no-brainer move of his own.
Hernandez only rounded third base by five feet, but Brown -- who didn't run hard out of the box -- tried to stretch his single. Curtis Granderson fired a one-bounce strike to catcher Travis D'Arnaud, who then threw it to second base. Brown found himself in no-man's land and was tagged out.
"[Brown] was thinking that there was a play at the plate, but Cesar had to freeze on the ball over [David] Wright," Sandberg said. "And then, [Brown] turned too wide. Cesar had to freeze there. It was high enough that he had a late break. As you get to the bag and round it, you pick up and see what's happening over at third base."
"I just saw the throw going over his head," Brown said. "I think I made the right read, only thing is I should have stayed in the rundown a little bit longer, see what can happen with maybe a bad throw or Cesar may score on that."
The fact that it's now June and Sandberg is still answering questions about his team's fundamentals speaks to their position in the lackluster National League East -- last place.
"Yeah, that's a frustrating part of it," Sandberg said. "Close games, extra-inning games, oftentimes you can look back at a play here or there just to get the job done. That's frustrating."
"[We've] got to be fundamentally sound to be a good ballclub," Brown said. "And we just have to keep battling and keep fighting to do the little things on the baseball field."
The Phillies had some lapses in the field, too. A Jimmy Rollins throwing error opened the door for Granderson's sac fly in the sixth, Reid Brignac bobbled a ball at third for the Phillies' second error, and Rollins was pulled off the bag on an easy double-play opportunity in the seventh.
"We'll continue to go out there and attempt to correct it," Sandberg said. "There's a game every day. There's a game to be played to clean it up and to play a solid game. And that's what it's going to take."
The one consistent bright spot for the Phils in this series has been their bullpen, and they were stellar again on Sunday until Duda's homer. Through the first three games of the series, Philadelphia relievers allowed only one run in 17 1/3 innings.
Cesar Jimenez, Jonathan Papelbon, and Justin De Fratus each delivered scoreless innings. Aumont retired the first two batters to face him in the 11th. Then, after walking the light-hitting D'Arnaud, Aumont surrendered the game-winner to Duda.
"If I pitch down, it's a different situation. But I left it up, [and Duda] hit it up," Aumont said. "Obviously, you know, I wanted to go out there and put up some zeros and let the guys hit. It's unfortunate, but it's just part of the game."
Hamels, meanwhile, did well to keep the Phils in it. The southpaw successfully danced around trouble in the seventh to finish his day. Hamels allowed two runs (one earned) on six hits and four walks, while striking out eight.
The Phillies are now 1-7 with the 30-year-old on the mound.
Hamels did not make himself available after the game.
"I mean, he gives us the opportunity. No question about it," Sandberg said. "We came up short on the offensive side for him, and he pitched well enough to win today."
The Mets seemed conscious of the Phillies' depleted bullpen, drawing out at-bats and working Hamels' pitch count. The Phils, however, were swinging at a lot of early pitches from Jon Niese, who left the game in the eighth inning after just 91 pitches.
"[Niese is] a strike thrower. He's quality left-hander. He establishes the strike zone," Sandberg said. "He doesn't walk many guys, and he's a tough lefty."
Offensively, Ryan Howard and Marlon Byrd provided the only sparks for the Phillies.
On a 1-0 fastball from Niese in the fourth with a man on, Howard teed off, sending the ball into the stands just to the left of the 409-ft. mark in center field for his 11th homer of the season.
Since Monday, Howard has four home runs and 14 RBIs.
Byrd tacked on another run in the 11th, with his eighth homer of the season. But it wasn't enough for the Phillies to erase the deficit.