"There's no doubt that we're struggling in some of these situations, but it's a long year," Yankees manager Joe Girardi said. "I believe more times than not, we're going to come through. Right now, they're struggling in those situations."
With Pelfrey limiting the Yankees to one run over six innings, Phil Hughes picked a bad time to run together back-to-back subpar starts, tempering his hot charge out of the gate this year as his team's fifth starter.
Hughes pelted himself for making catcher Francisco Cervelli's glove jump too much within the strike zone, a sign that he did not possess sharp command of his pitches -- something he also felt in his previous start, against the Red Sox.
"We need to win games," Hughes said. "That's what it comes down to. I could have pitched great, but if we lose, we lose. I need to be better -- that's the bottom line. These last couple of outings, I haven't been good with my command. It's something I need to work on."
While Hughes went a little deeper and contained the Mets a little better on Saturday, it wasn't by much. Making his first Subway Series start and third appearance, Hughes gave up four runs on eight hits in 5 2/3 innings, walking three and striking out seven in his first losing effort of 2010.
"It seems like the last couple of outings, I get a quick two outs and can't put the inning away," Hughes said. "They took advantage, and it was too much for us.
"I just haven't executed pitches when I've needed to with two outs, and unfortunately they've strung some hits together. They made me pay for it."
The Mets got two quick runs off Hughes in the first inning -- the biggest deficit he'd faced all season -- and started the damage with two outs.
Jason Bay connected for a double and scored on David Wright's run-scoring single. Angel Pagan drove in Ike Davis with a broken-bat single to left, ending the inning when Wright was thrown out advancing to third.
"He's a tough pitcher," Pagan said. "He's got great stuff, but we put some good at-bats against him and we beat him."
After getting the first two outs of the third, Hughes permitted a single to Bay -- part of a four-hit night for the left fielder -- that would cost him. Davis walked and Wright bashed a run-scoring single, immediately following a visit from pitching coach Dave Eiland.
"He wasn't bad," Girardi said of Hughes. "The frustrating part for him was the two rallies that they were able to come up with, with two outs. It has to be frustrating with nobody on."
Hughes was also let down by his defense in the sixth inning on a play that made it 5-1 at the time. Pagan lifted a fly ball to left that Randy Winn lost, allowing the ball to bounce for a double, and Pagan would score when Alex Cora smacked Hughes' 117th and final pitch through the right side for an RBI.
"I ran toward the line and I missed it," Winn said. "It's as simple as that. It's a play I should have made, and I didn't make it. ... I looked down to kind of check how close I was getting to the line, and when I looked up, the ball wasn't where I thought it was going to be."
Even the Yankees' run-scoring hit off Pelfrey wasn't exactly a scorcher. Cervelli accounted for that one with a sixth-inning tapper to the mound that struck the pitcher's right foot, allowing Robinson Cano to score from third base.
"You can't take all the blame or give all the credit to one side," said slumping first baseman Mark Teixeira, who ran his skid to an unsightly 1-for-23. "Those pitchers pitched really well tonight. Pelfrey was great.
"When they needed to make big pitches with runners on base tonight, they made them. So give them credit. But the same time, maybe if we have a little better swings, a little better at-bats, maybe we break through."
Chan Ho Park allowed an RBI single to Pagan in the seventh for a Mets insurance run, which would prove helpful.
The Yankees loaded the bases against Pedro Feliciano in the eighth. Fernando Nieve struck out pinch-hitter Juan Miranda, but Kevin Russo worked a full-count walk to force in the second run.
Derek Jeter cut the Yankees' deficit to 5-3 with a fielder's-choice grounder against Francisco Rodriguez, but that would be as close as the Yanks could get.
With Rodriguez trying to convert a five-out save, Alex Rodriguez notched a one-out single and Nick Swisher connected for a two-out hit that put the tying run aboard.
But the Mets' closer got Cervelli to offer at strike three, as the Yankees lost for the first time in five contests at Citi Field.
"You can look at all the wasted opportunities that we had," Girardi said. "It's the difference in the game."