That tough break had no effect on Peavy's jubilant mood.
"This is the most gratifying win I think I've ever been a part of as a Padre, watching the total team effort that we gave tonight result in a win," Peavy said.
Peavy settled down after allowing Carlos Delgado's long three-run homer in the first and surprising San Diego held on for its sixth win in seven games. Former Mets reliever Heath Bell pitched a perfect ninth for his fifth save in five chances.
The Padres looked right at home in New York's sparkling new yard, with its expansive outfield reminiscent of the power alleys in their Petco Park. They only needed one extra-base hit to send the Mets to their fifth loss in seven games.
"The ballpark is beautiful. They did it right, other than getting some hot water down in the clubhouse, we'd be set," a chuckling Peavy said. "But, nah, beautiful facility."
Delgado hit his third homer with one out in the first, sending a 3-0 pitch over a billboard hanging above the bullpens in right-center. Ramon Castro hit a two-run shot off former teammate Duaner Sanchez in the eighth but that was it for New York.
The Mets put runners on second and third in the third and fourth innings and couldn't come up with a big hit. Peavy struck out Castro to end the third, and fanned David Wright to end the fourth after a fan scooped up Daniel Murphy's double down the line to keep Jose Reyes at third.
"We continue to put ourselves in good position to win but we haven't been able to finish," manager Jerry Manuel said.
Peavy (2-1) allowed three runs and six hits in the finale of the three-game set. He struck out five and walked four.
The 2007 NL Cy Young Award winner also helped out at the plate, setting up San Diego's five-run third inning with a key sacrifice that put runners on second and third. Jody Gerut and David Eckstein followed with RBI singles to cut the Mets' lead to 3-2.
John Maine (0-1) got Brian Giles to ground out to first, but Gerut and Giles each moved up a base. After Adrian Gonzalez was walked intentionally, Headley lined a two-run single into center field to put San Diego ahead 4-3. Kevin Kouzmanoff tacked on another RBI single as the crowd of 35,985 groaned.
"Adrian is such a great player that that's going to happen," Headley said. "They're going to make the younger, less established players beat them. Today I was behind him and it was just a big hit. You want to come through so Adrian is going to get his chance to hit."
Headley also doubled in Gonzalez in the fifth and led off the eighth with another single to tie his career high for hits set Sept. 19 at Washington.
Maine allowed six runs and seven hits in five innings. He struck out four and walked three.
"As is so often the case, it was one inning," he said. "I made some good pitches but they hit them. It's frustrating."
Ryan Church and Luis Castillo each had two hits for New York, which will host Milwaukee this weekend in their second regular-season series at Citi Field. Former Mets manager Willie Randolph, fired in the middle of last season, is in his first year as Milwaukee's bench coach, adding more intrigue to the matchup.
"I'm looking forward to seeing him," said Manuel, who was promoted from bench coach after Randolph was dismissed. "I'm excited that he's back in baseball. He's a bench coach and I know at some point that he'll get another opportunity [to manage] and I know he'll do well."
Mets RHP Mike Pelfrey played catch before the game and downplayed the forearm tendinitis that led the team to send him for an MRI exam Tuesday. "I'm not concerned about it at all," he said. "I'm going to be OK." Pelfrey wants to start Sunday against Milwaukee but Manuel was waiting to see how he responded to anti-inflammatory medication before making a decision. ... Padres RHP Walter Silva will miss his next scheduled start with a strained right forearm. The 32-year-old rookie was injured while batting in the second inning of the Padres' 6-5 victory over the Mets on Monday night. Black said the club is still working out who will start Sunday at Philadelphia. ... The Padres were without first base coach Rick Renteria, who was attending to a family matter in Southern California and isn't expected to be with the team this weekend. Hitting coach Jim Lefebvre subbed for Renteria against the Mets. ... Mets C Brian Schneider (tight back) rested.