"My last couple starts have been embarrassing," Pelfrey said. "I know I need to be a lot better and I'm going to be a lot better."
Following his previous start, the 25-year-old Pelfrey had a long chat with manager Jerry Manuel that the pitcher described as "all positive."
"He told me he expected more out of me and I told him the same thing. I said, 'Hey, your expectations aren't higher than mine,'" Pelfrey said. "I can finish this thing on a positive note."
Pelfrey (10-10) allowed five hits in his longest outing this year and Murphy finished a double shy of the cycle. The Mets took two of three from Chicago in a series between preseason NL favorites who have struggled all year.
It was the first time New York won a series since taking three of four games against Colorado from July 27-30. The injury-depleted Mets went 0-8-2 in series during that span.
Francisco Rodriguez, pitching on his bobblehead day, allowed a run in the ninth before nailing down his 30th save in 35 chances.
Manuel and a trainer came out to check on Rodriguez after Geovany Soto's two-out RBI double, but the All-Star closer waved them off and got pinch-hitter Kosuke Fukudome to ground out on his next pitch.
Rodriguez said his left leg simply cramped up.
"I probably didn't get enough water," he said.
Soto had a pair of run-scoring doubles for the Cubs, who mustered little offense in support of Randy Wells (10-8). A contender for NL Rookie of the Year, he yielded two runs -- one earned -- and seven hits over six innings in a hard-luck loss.
"There's no sense in talking about it," Cubs manager Lou Piniella said. "Wells did a nice job again. He's been one of the most positive developments here."
Chicago starters have a 0.70 ERA in the last six games, but the team is only 3-3 during that stretch.
A 13-game winner last season, Pelfrey entered 1-4 with a 6.09 ERA in his past six starts. But he was rarely in trouble Sunday. He struck out five, walked one and threw 70 of his 105 pitches for strikes.
"He was tremendous. He was rolling. He was throwing every single pitch for strikes," Rodriguez said. "He was the Mike Pelfrey that everybody was hoping to see."
After Soto's RBI double with nobody out in the fifth, the big right-hander retired his next three batters to limit the damage.
"From here on out I think we'll see pretty good efforts from Mike," Manuel said.
Murphy hit a solo homer into the second deck in right field in the fourth. A two-out error by third baseman Aramis Ramirez extended the New York fifth, and Murphy made the Cubs pay for their mistake with a tiebreaking RBI single.
"You've got to pitch around the error. That's what good pitchers do and I didn't," Wells said.
Cubs shortstop Andres Blanco turned in a spectacular play in the fourth to rob Jeff Francoeur of a hit. Blanco made a diving stop up the middle and threw to first from the seat of his pants as he rolled over on the outfield grass.
"That's as good a play as I've ever seen made at the major league level," Piniella said.
Mets CF Carlos Beltran went 1 for 5 at Class A Brooklyn, striking out three times. He said he was ready to rejoin the Mets on Tuesday. ... Chicago recalled RHP Esmailin Caridad from Triple-A Iowa. Piniella said Caridad would go into the bullpen but could get a spot start or two before the seasons ends. He said the team might also want to take another look at RHP Jeff Samardzija as a starter before the end of the year. Samardzija, currently pitching at Iowa, was a star receiver at Notre Dame. ... Piniella rested Fukudome and SS Ryan Theriot. ... Piniella said he thinks the Cubs, last in the majors in stolen bases, will try to add some speed in the offseason. ... Chicago 1B Derrek Lee turned 34. ... Cubs RF Milton Bradley hobbled around after fouling a ball off his right foot in the fourth. He was checked by a trainer and Piniella, but stayed in the game. ... Rodriguez's 238th save broke a tie with Ugueth Urbina for most by a Venezuelan-born pitcher.