Halladay, 4-1 in his last six starts, is 110-0 when he is staked to a lead of at least four runs. Halladay (9-7) scattered eight hits over 7 1-3 innings, allowing one run with five strikeouts and one walk. Philadelphia won two of three in the series against the NL Central leaders.
All-Star first baseman Joey Votto returned to the Reds lineup for the first time since July 15 and lined the third pitch he saw in 52 days to left field for a single with two outs in the first inning.
The Reds went 32-16 while Votto was out due to two operations related to a torn meniscus in his left knee. Votto finished 2-for-3 with a walk and a strikeout for Cincinnati, which lost a series for just the third time in 16 matchups since the All-Star break (11-3-2).
Jay Bruce homered for the fourth consecutive game, but it wasn't enough to rally the Reds in the ninth inning.
For the second time in less than three weeks, Reds starter Mike Leake was roughed up by the Phillies. After giving up a career-high seven runs in 4 1-3 innings in Cincinnati's 12-5 loss at Philadelphia on Aug. 20, Leake (7-9) was touched for six more in just 2 1-3 innings on Wednesday. He gave up six hits with a walk and a strikeout.
The Phillies opened the second inning with consecutive singles by Ryan Howard, John Mayberry Jr., and Domonic Brown before Kratz hit a 2-2 pitch into the left-field seats for a three-run homer, his ninth shot of the season.
Leake was knocked out of the game in the third inning after he issued a leadoff walk to Juan Pierre and gave up Utley's 10th homer of the season, a 414-foot drive to center field on the first pitch.
Reds manager Dusty Baker pulled Leake from the game after Howard flew out to the warning track in left field, and Mayberry lined a double off the top of the left field wall.
Bruce drove in both Reds runs. He doubled with two outs in the fourth to drive in Chris Heisey, and led off the ninth against Phillies closer Jonathan Papelbon with an opposite-field shot for his 32nd homer of the season.
Notes: Brown snapped a 0-for-19 slump with his second-inning RBI single. ... The Phillies finished 4-3 against the Reds this season. Philadelphia has won nine consecutive season series against the Reds since Cincinnati went 5-4 in 2003. ... Reds SS Zack Cozart missed his second consecutive start because of a sore back, Baker said. Didi Gregorius made his major league debut by starting in Cozart's place. ... Cincinnati and Philadelphia both have Thursday off. The Phillies face Colorado on Friday in the first game of a six-game homestand. The Reds will open a three-game home series against Houston on Friday.