Jimmy Rollins had an RBI single to help the Phillies win for the 11th time in 12 games and go 36 games over .500 (76-40) for the first time since 1977, when the team finished 101-61 and lost to the Dodgers in the NL championship series.
Philadelphia maintained its 8½-game lead over Atlanta in the NL East.
Lee (12-7) allowed four singles and only two runners past first base. The left-hander's previous outing against the Dodgers - a 3-1 win on June 6 - began an incredible month for the three-time All-Star in which he became the first Phillies pitcher to throw three consecutive shutouts since Robin Roberts in 1950.
Ryan Madson got three outs for his 21st save in 22 chances, despite allowing an RBI single in the ninth by Casey Blake.
Coming off a 3-0 victory last Thursday at San Francisco in which he threw 106 pitches and posted his major league-leading fifth shutout, Lee raised his strikeout total to 177 - eight shy of his career-best total from last season.
Lee fanned Matt Kemp and Andre Ethier their first two times up en route to his 17th career double-digit strikeout game and eighth this season - the most by a Phillies pitcher since 1988, when Curt Schilling did it 15 times.
Lee homered with one out in the seventh against lefty Ted Lilly, who has given up a team-high 25 this season. Lee, who spent most of his 10-year career in the American League, did not have a home run in 51 career at-bats entering this season. His first one came July 9 against Atlanta's Tommy Hanson in a no-decision at Philadelphia.
Lilly (7-12) allowed two runs and six hits over eight innings with five strikeouts and a walk. The left-hander retired NL RBI leader Ryan Howard on inning-ending groundouts his first two times up - both times with two men on base.
Rollins lined a soft opposite-field single over the head of first baseman Blake in the third inning to drive in Wilson Valdez with the Phillies' other run.
Shane Victorino was hit by Lilly's next pitch, but went straight to first base without incident. Victorino touched off a benches-clearing incident last Friday night at San Francisco after he was plunked by Ramon Ramirez, and has played two games since appealing the three-game suspension he received from Major League Baseball.
Lilly gave up singles to his first two batters of the game before rookie shortstop Dee Gordon executed an unassisted double play on Chase Utley's low line drive - short-hopping the ball and tagging lead runner Rollins before stepping on second for the force on Victorino. Utley stole second before Howard grounded out against the shift.
The first two Dodgers got hits in the bottom half, including a bunt single by Jamey Carroll that put runners at the corners after Gordon stole second. But Lee struck out Ethier and Kemp, then retired Aaron Miles on a foul pop to first base after Carroll stole second.
Notes: The Dodgers held a special pregame ceremony to honor Hall of Famer Duke Snider, the center fielder on Brooklyn's only World Series championship team, who died Feb. 27 at age 84. Tuesday was 58 years to the day that Snider hit a tiebreaking grand slam off Joe Nuxhall at Cincinnati's Crosley Field to snap a scoreless tie in a 9-1 Dodgers win - the first of only three slams Nuxhall would give up in his 16-year career. ... Phillies 2B Chase Utley is one game away from tying Tony Taylor's franchise record of 1,003 games at that position. ... Lee, Roy Halladay and Cole Hamels are among the top five pitchers in the majors this season in strikeout-to-walk ratio. ... Rollins' next triple will make him the fourth player in Phillies history with at least 100 in the regular season. That list includes Ed Delahanty, Sherry Magee and Sam Thompson - all of whom played for them before 1915. ... Manuel played in 19 games with the Dodgers between 1974 and 1975, going 3 for 18 with three RBIs - all as a pinch-hitter for manager Walter Alston.