Both teams showed an early nickel-and-dime attack. The game's first 21 hits were singles. That all changed in the sixth inning when Giants shortstop Adam Duvall hit a two-run home run to center field to give San Francisco a 5-4 lead.
Duvall, who made his major-league debut on June 26, entered the game with one home run and one RBI in 18 at-bats.
Former Phillie Hunter Pence added an RBI single in the sixth, extending the lead to 6-4 and ending Lee's evening.
Lee refused to blame his troubles in the sixth inning on fatigue.
"No, that wasn't a factor at all," said Lee, who threw 90 pitches, 59 for strikes.
Phillies manager Ryne Sandberg concurred.
"He felt good out there," Sandberg said. "When I went out to get him, he still felt like he had something left in there."
While fatigue wasn't a factor, Lee said that rust clearly was.
"Yes, a little bit," he said. "I wasn't locating that well and I was behind in the count more than I would like to be."
His velocity was in the 90 m.p.h.-range, but his command wasn't sharp.
"When he was throwing strikes, he seemed to not be on the corners," Sandberg said. "[It was] not the command he normally has; balls were over the plate."
Lee also gave credit to the Giants.
"I wasted a lot of pitches early, and they weren't really competitive pitches," he said. "They earned it as well; they got 12 hits off me."
The 12 hits he allowed tied a career high for Lee.
The Giants opened the scoring on Gregor Blanco's RBI single to right in the second. On the same play, the inning ended when rightfielder Marlon Byrd nailed Mike Morse at the plate.
The umpires reviewed a home-plate collision in which Morse flipped over catcher Cameron Rupp. The call on the field was upheld.
Jimmy Rollins delivered a two-run single to left field in the second, giving the Phillies a 2-1 lead against starter Ryan Vogelsong, the Octorara High product.
The Giants regained the lead on Buster Posey's two-run single to center in the third.
Lee got out of a bases-loaded, one-out jam in the fourth. Vogelsong grounded to Cody Asche at third, who got the force at home for the second out. Asche saved at least one run when he made an outstanding diving stop to his left of a Pence grounder and got the force at second base.
The Phillies then took a 4-3 lead on Ryan Howard's checked-swing two-run single to left in the fourth before the Giants chased Lee with three runs in the sixth.