"Starting to roll a little bit," Mets manager Willie Randolph said. "Hopefully, we're ready to take off."
Ryan Church also hit a home run and Moises Alou drove in three runs for the Mets, who beat Chien-Ming Wang and won a series at Yankee Stadium for only the second time since interleague play began in 1997. They took two of three in 2005.
This one was a two-game sweep after Johan Santana beat the Yankees 7-4 on Saturday. The scheduled opener Friday night was rained out and is likely to be made up when the teams meet again June 27-29, possibly with a two-ballpark doubleheader.
When the Mets showed up Friday, they had just lost three of four at home to last-place Washington, and Randolph was under fire. So they cleared the air in a closed-door meeting following remarks by closer Billy Wagner that some perceived as critical of his teammates.
"The positive energy that comes from winning here," David Wright said, "I think that can give you a lot of momentum."
Perez (4-3) pitched three-hit ball for a season-high 7 2/3 innings, handing the Yankees their fifth loss in six games. The so-called Bronx Bombers, missing injured sluggers Alex Rodriguez and Jorge Posada, have scored only 12 runs during that stretch while falling to a season-worst 20-24.
The margin Sunday night could have been bigger, too, if not for a blown call that cost Carlos Delgado a three-run homer. Perez won his second successive outing following a three-game skid, and the Yankees dropped to 4-10 against left-handed starters.
"We all have to do better. It starts with me. Put it on me," manager Joe Girardi said. "I'm the leader. I've got to find something."
Rodriguez is expected to return Tuesday night against Baltimore.
"It was pretty embarrassing. We're much better than what we're showing," Johnny Damon said. "Nothing should matter to this offense. We've got too many All-Stars around, too many talented players. We just need to be better."
Wang (6-2) gave up seven runs and six hits in 7 2/3 innings, falling to 0-2 in his past three starts. Hideki Matsui homered for the Yankees.
The Mets loaded the bases in the fourth and took the lead on Church's RBI grounder. Alou followed with a two-run single to right on a half-swing, and Delgado sliced a line drive down the left-field line that should have been a three-run homer.
The ball barely skimmed over the wall, right above the white foul line painted on the padded blue fence, and glanced off the bottom of the foul pole, which is set back just a bit from the wall.
Third base umpire Mike Reilly originally signaled home run, but shortstop Derek Jeter argued and the umps quickly huddled before reversing the call -- foul ball. Mets manager Willie Randolph argued to no avail.
"My three partners were adamant that the ball was foul," Reilly said. "It was a tough call to make. We try to get every play right."
Sitting next to the foul pole, fan Chris Rom picked up the ball after it hit him in the hip and was soon showing television cameras the mark Delgado's shot left on the pole -- and the smudge on the ball, too.
"It was a home run. It's indisputable. That's why you need replay for home runs," said Rom, a Mets fan who works in Brooklyn. "CSI can come take DNA off the pole -- it was a home run."
As Delgado continued his at-bat, Mets bench coach Jerry Manuel kept barking and pointing at plate umpire Bob Davidson, who shouted back and ejected Manuel.
Delgado ended up hitting an RBI single that made it 4-0.
"I'll take one if I can't have three," he said.
Jeter singled in the bottom half and Matsui followed with his sixth home run.
Church connected leading off the sixth to make it 5-2, the second home run Wang has allowed in 10 starts this year. Wright hit a leadoff double in the eighth and scored on Alou's shallow sacrifice fly, chasing Wang.
- Marlon Anderson started in LF for the Mets and Alou was their DH because Alou's 41-year-old body has felt sore lately.
- Jeter got his first stolen base of the season.
- Injured C Jorge Posada (right shoulder) began catching bullpen sessions in an attempt to speed up his rehabilitation. Posada also made throws from 75 and 90 feet, and hopes to return to the Yankees by early June.
- The Yankees began the day 12th in the AL in runs with 177.
- Church scored three times and made a sliding catch in RF to save a run in the second.