"I think when you go up against your rival, you have a little extra adrenaline and you're into the game," Pelfrey said.
Francoeur had three hits, Francisco Rodriguez escaped a ninth-inning jam and New York took the opener of a four-game series that's lost most of its luster. Ravaged by injuries, the Mets have faded to fourth in the NL East, 13½ games behind the division-leading Phillies.
Pelfrey (9-8) tossed six solid innings and got strong relief work from New York's bullpen, making him 3-0 with a 3.92 ERA in four starts against Philadelphia this season. He is the only major league pitcher with three wins against the Phillies this year.
Pedro Feliciano and Brian Stokes combined for two scoreless innings before handing the ball to Rodriguez. With runners at the corners, the All-Star closer struck out Chase Utley and Ryan Howard for his 27th save in 32 chances.
Hamels (7-8) allowed 10 hits in five innings before he was lifted for a pinch hitter. The World Series MVP is 0-3 in four August outings.
"That's kind of the game I've seen him pitch now the last three or four times out," Phillies manager Charlie Manuel said. "It's just a matter of getting more consistent, putting a couple good outings back to back. It's a feel. And like right now, he lacks his, what I call his real good feel and his smoothness and his command of pitching."
Since beating the Mets in his first start against them, Hamels is 0-4 with a 5.40 ERA in nine starts vs. New York. The left-hander called the Mets "choke artists" in the offseason, referring to their September meltdowns the past two years.
Francoeur was well aware of that, even though he wasn't acquired from Atlanta until last month.
"I heard it," he said. "We ain't going to lay down."
Only three umpires worked the game because weather-related travel problems prevented crew chief Rick Reed from arriving at Citi Field in time. Nonetheless, Mets manager Jerry Manuel and outfielder Gary Sheffield got ejected.
The start was delayed 76 minutes by rain. Once play began, the Mets announced that Reed, who had been scheduled to umpire third base, was unable to get to the ballpark. Mark Wegner shifted from second base to third - when no runners were on base. Tim Timmons remained at first and Rob Drake behind the plate.
"It's not something we want," Wegner said. "There's a reason there's four guys out there."
Francoeur tried to steal second in the fifth and was called out by Wegner, even though replays showed that shortstop Jimmy Rollins missed the tag following a high throw. Francoeur protested and Jerry Manuel came out of the dugout for an animated argument before he was ejected by Wegner.
"We've got to continue to fight as best we can," Jerry Manuel said. "When we feel that things are against us, we've got to continue to stand up against those things."
Drake tossed Sheffield in the seventh when he flipped his bat after getting called out on strikes.
Pedro Feliz's RBI single cut it to 4-2 in the sixth and Philadelphia loaded the bases after Mets second baseman Luis Castillo failed to cover first on a sacrifice bunt. It was the second time in three games that Castillo hasn't covered a base in time.
Pelfrey, however, escaped further damage by inducing consecutive popups from pinch-hitter Ben Francisco and Rollins.
"That's what won the game for him," Charlie Manuel said.
Fernando Tatis tripled in the second for New York and scored on Daniel Murphy's groundout. After Hamels hit Pelfrey on the left arm with an 0-2 pitch, Angel Pagan added a two-out RBI single.
Francoeur homered leading off the third and Omir Santos hit a foul sacrifice fly behind first that was caught by Howard as he leaned into the stands.
"It was just a case of not making the right pitches at the right time," Hamels said.
NOTES: Phillies 3B Greg Dobbs left in the fourth with a strained right calf. He was replaced by Feliz. ... Pelfrey plunked Jayson Werth on the left wrist in the sixth. ... Stokes has a 0.52 ERA in his past 19 games. ... Castillo had his fourth consecutive multihit game. He is batting .452 in his last 12. ... Jerry Manuel has been ejected four times this season.