The Yankees went 0-for-9 with runners in scoring position against Boston pitching, producing just Curtis Granderson's team-leading 32nd home run, a solo shot off Lester in the fourth inning.
New York knocked on the door in the ninth inning against Alfredo Aceves, but the former Bronx Bomber closed out his 25th save as the Yankees left a total of six men on base.
"It's hard to win games when you do that," Yankees manager Joe Girardi said. "When you have some opportunities, you're not able to score runs and tie the ballgame up if you have a chance. When you don't do that, usually you're going to lose games."
Lester has battled an inconsistent season that included a seven-start winless streak but has now pieced together back-to-back victories and improved to 7-2 with a 3.70 ERA in 12 career starts in the Bronx.
"He had the cutter working, which is his signature pitch," Granderson said. "It's got a lot of movement on it. Any time it sweeps as far across as it does, it makes it very difficult to hit."
Rookie right-hander David Phelps went unrewarded for a quality start as the Yankees continue to patch their rotation without the services of ace CC Sabathia, who expects to return from the disabled list on Friday against the Indians in Cleveland.
Phelps limited the Red Sox to three runs over 6 2/3 innings, marking the deepest he has pitched in his five big league starts to date.
"It felt great," Phelps said. "I'd like to, one of these days, finish the seventh inning. My two [recent] starts in the Minor Leagues, I went 6 2/3 in both of those. I felt great. I had some quick innings. The first inning got me a little bit, but I still went out there and gave us a chance."
Gonzalez's 14th home run of the season was Boston's big blow, and Girardi marveled that it hadn't come on a bad pitch, slugged on a fastball that was low and off the plate.
"I thought [Phelps] mixed his pitches well," Girardi said. I thought he used everything that he had, and even the home run that he gave up, it was a ball off the plate. It wasn't even a strike that he gave up, so I thought he did a really good job."
Following that blast to left field with Carl Crawford aboard, Phelps settled in, limiting Boston to just Nick Punto's fifth-inning RBI double the rest of the way.
Phelps walked none and struck out seven in a career-high 95-pitch effort, his second solid start in place of Sabathia. Despite that showing, Phelps appears ticketed back to a swingman role in the bullpen come Friday.
"I'm just going to show up tomorrow and do my work and go from there," Phelps said. "I'll think about the next day when it comes. I'm not going to be able to do what [Sabathia] does, but I just go out there and try to keep us in the game every time my name's called. Hopefully, I keep doing it."
Swisher and Granderson accounted for four of the five hits permitted by Lester, who walked two and struck out four to reduce his ERA 17 points from 5.20.
"You weren't getting on tonight unless you were getting a base hit," Swisher said. "He was really pounding the zone and really did a good job for them."
An eighth-inning single off Boston's Andrew Bailey improved Swisher's performance to 3-for-4 for the afternoon; as Swisher comes down the stretch in a contract year, the switch-hitter appears primed for a strong finish.
"I've just kind of been thinking a lot," Swisher said. "That word 'regret' pops in my head. That's the last thing that I want to have, regardless of whatever my situation is next year. I want to enjoy this time that I have now and just soak it up and see what happens."
Of more immediate concern than next year's payroll, the Yankees continued to have trouble finding ways to retire shortstop Pedro Ciriaco, who is quickly earning a reputation as a Yankees killer.
"You think they are going to try to trade for him?" Red Sox manager Bobby Valentine said.
Ciriaco had four hits and a run scored for the Red Sox, marking the fourth game in seven starts against the Yankees this year that he's recorded three or more hits. He is an improbable 15-for-29 against Yankees pitching this year.
"I feel like any part of the plate we throw the ball at, he's getting the bat on it and getting a hit," Phelps said. "He bunts, and it's a perfect bunt. The guy's on fire against us."