Raul Ibanez hit a three-run homer for the Phillies, who took three of four from the Reds.
Both teams were playing with little rest following Wednesday's 19-inning marathon ended at 1:19 a.m., after 6 hours, 11 minutes and 600 total pitches.
Every Phillie had at least one hit on Thursday, including Chase Utley, who is 2 for 14 since returning from the disabled list earlier this week.
The Phillies' offense gave Lee a 1-0 lead in the first inning when Ryan Howard doubled in Michael Martinez with two outs.
Howard was intentionally walked in the fourth inning with two outs and a runner on second, but Ibanez hit an 0-2 pitch for a home run. Ibanez is batting .361 (30 for 83) since snapping an 0-for-35 skid.
The Reds cut it to 4-2 in the fourth on Paul Janish's two-run single that scored Miguel Cairo and Jay Bruce.
Bruce tied the game with a two-run homer to right in the sixth inning. The shot was his National League-leading 14th of the season. Bruce has batted .486 with six homers and 14 RBIs during an eight-game hitting streak.
Reds starter Homer Bailey allowed four runs and five hits and a walk in four innings, and left the game with right shoulder spasms suffered during a fourth-inning at-bat.
Lee (4-4) threw 114 pitches in eight innings. But his biggest contributions came at the plate.
The Phillies loaded the bases with no outs in the sixth inning against Daryl Thompson (0-1), who had made his major league debut an inning earlier.
Lee followed up a walk to catcher Dane Sardinha with a first-pitch double over the head of center fielder Drew Stubbs. It bounced over the fence for a ground-rule double. An inning later, his single up the middle scored John Mayberry Jr.
Lee became the first Phillies pitcher to drive in three runs since Cory Lidle, on Sept. 4, 2004, against the Mets.
Wilson Valdez, who became the first player to start a game in the field and later earn the win as a pitcher since Babe Ruth on Oct. 1, 1921, received a standing ovation when he batted in the second inning.
Right-hander Jose Contreras, activated from the 15-day disabled list before the game, worked a scoreless ninth inning.
Notes: OF Shane Victorino (right hamstring) is scheduled to begin a rehabilitation assignment on Saturday with Class A Lakewood. He is also scheduled to play there Sunday. ... Reds utility player Miguel Cairo batted cleanup for the first time this season. ... RHP David Herndon was optioned to Triple-A Lehigh Valley to make room for Contreras. The Reds placed Matt Maloney on the 15-day disabled list, retroactive to Tuesday, with a strained left oblique muscle.