With last year's NL East champions missing their MVP shortstop, the Mets won the final two of a three-game series after losing nine straight to Philadelphia -- including the final eight meetings in 2007.
"The way that we won I think gives us some momentum and hopefully we can use that going forward," David Wright said. "Everything was extremely negative after that first loss. To come and take this series after dropping that first one hopefully gives us some confidence."
With two outs in the 12th, Reyes doubled off Tom Gordon (0-2) and Pagan grounded a sharp single to center for his third hit.
Jayson Werth's strong throw home made it a surprisingly close play on the speedy Reyes, who slid around catcher Chris Coste and appeared to touch the plate with his left hand just before Coste applied the tag.
Plate umpire Ted Barrett immediately signaled safe, and Phillies manager Charlie Manuel popped out of the dugout for a brief argument as the Mets celebrated nearby.
"Safe, yes," Reyes said. "He hit the ball hard and they were playing kind of shallow. He made a perfect throw. It made the play closer than I thought."
After watching the replay, the Phillies disagreed with the call.
"The guy was out," Manuel said. "He didn't make it. Maybe Ted wanted to go home. He told me he got there first. Maybe he ought to go look at it."
Rollins was missing from the starting lineup for the second consecutive game because of a sprained left ankle. He struck out as a pinch hitter against Billy Wagner leading off the ninth.
Jorge Sosa (1-0) retired Feliz with one pitch in the 12th to earn the win. The Phillies stranded 13 runners for a total of 35 in the series.
"We had plenty of opportunities. We left a lot of guys on base. We didn't get it done when we had to," Manuel said.
The Phillies rallied and played errorless ball one night after a sloppy performance without Rollins. Eric Bruntlett filled in at shortstop again after making two of Philadelphia's four errors Wednesday night -- both in a six-run third inning.
With two on and none out in the 11th on Thursday, Bruntlett struck out trying to bunt.
Maine took a 3-0 lead into the seventh before giving up a leadoff homer to Feliz, his first with the Phillies, and Coste's double off the left-field fence.
Pedro Feliciano pitched New York out of a jam with three straight strikeouts, but Heilman squandered the lead in the eighth.
Howard opened the inning with a 450-foot shot to center, his second home run of the season. Pat Burrell walked and pinch-runner So Taguchi went to third on Geoff Jenkins' single. Feliz drove in the tying run with a slow groundout before Heilman escaped further damage.
Ryan Church's two-run single with two outs in the fourth put New York ahead, and Carlos Beltran added an RBI single off Adam Eaton in the sixth. Pagan also doubled and scored twice in another fine game while filling in for injured left fielder Moises Alou.
"Angel Pagan has done a great job for us," manager Willie Randolph said. "He's a high-energy guy. He's playing with a little confidence right now. He had a great spring. He's been in the middle of a lot of things going on the last week or so."
Eaton is 5-0 with a 2.90 ERA in eight starts against the Mets, including 4-0 with a 3.08 ERA in six starts at Shea Stadium. Maine is 4-0 with a 2.05 ERA in seven starts against Philadelphia.
Wagner also fanned Howard in a hitless ninth. Wagner's only other appearance this season was April 2. ... Reyes and Wright pulled off a double steal in the eighth. It was Reyes' first stolen base since Sept. 15. The 22-game drought was the longest of his career. ... With nobody left on the bench besides regular catcher Carlos Ruiz, Manuel used pitcher Cole Hamels as a pinch hitter in the 11th and sent him up to bunt. Hamels got a bunt single when catcher Brian Schneider slipped as he picked up the ball. It was the first pinch-hit by a Phillies pitcher since Omar Olivares hit a two-run homer against Colorado on July 24, 1995.