Utley raised his average to .500 through 10 games, with six doubles, three home runs and 10 RBIs. The five-time All-Star, who missed two games with the flu, has a hit in each of his games this season.
Will Nieves had three hits and two RBIs for Philadelphia, which has won 13 of the last 16 games against Miami.
Garrett Jones homered and Casey McGehee had two hits and an RBI for the Marlins, who lost their seventh straight.
Utley broke a 3-all tie with two outs in the eighth by driving a 1-0 offering from Mike Dunn (0-1) into the seats in right-center.
A.J. Bastardo (1-1) pitched a scoreless eighth for the win.
Jonathan Papelbon pitched a scoreless ninth for his third save in four chances.
Kyle Kendrick owns a sparkling career record against the Marlins, going 12-2 with a 3.48 ERA in 21 career games coming in. In his last 11, he was 9-0 with a 2.21 ERA. But he did not factor into the decision Sunday after giving up three runs - two earned - on six hits in six innings.
His counterpart, Henderson Alvarez, also didn't get a decision after yielding three runs and 12 hits in six innings.
The Marlins took advantage of first baseman Ryan Howard's fielding error to get a run in the first on McGehee's RBI single and tacked on run on in the second on Christian Yelich's run-scoring single.
Jones launched his first homer of the season to deep right with one out in the fifth to give Miami a 3-1 lead.
But the Phillies tied it in the bottom half on Nieves' two-out, two-run double to right.
The Phillies requested an out call at home plate be reviewed in the seventh inning.
Tony Gwynn Jr. was called out trying to score from first on Utley's double to left. But manager Ryne Sandberg asked for the play to be reviewed likely because catcher Jeff Mathis was blocking the plate with his left leg prior to Gwynn's slide.
Under the new replay rule, umpires initiate a review of the new rule regarding collisions at home plate.
After a 54-second delay, though, the out call by homeplate umpire Mark Ripperger was upheld.
Howard had just three hits in his last 17 at-bats before homering to the opposite field with one out in the third to tie it at 1. It was the second homer of the season for Howard.
Gwynn started in center field in place of Ben Revere for the third straight game and had three hits. Revere struck out swinging in the seventh as a pinch-hitter.
The Phillies, who entered leading the NL with 43 bases on balls, walked six times against three Marlins pitchers.
NOTES: Philadelphia Hall of Fame third baseman Mike Schmidt debuted in the Phillies broadcast booth during the game. Schmidt will serve as a color analyst on Sunday home games this season. . Prior to the game, the Phillies optioned RHP Justin De Fratus to Triple-A Lehigh Valley and recalled RHP Luis Garcia. De Fratus allowed four runs in five innings (7.20 ERA) over four games this season. . Phillies RHP Roberto Hernandez (1-0, 4.35) opposes Atlanta RHP Ervin Santana (1-0, 0.00) when the teams open a four-game series in Philadelphia at 7:05 Monday night. . The Marlins return home for a three-game set against Washington, beginning on Monday when Nationals RHP Jordan Zimmerman (0-0, 8.10) faces LHP Brad Hand (0-0, 3.24). . Philadelphia 3B Cody Asche went 0 for 2 and is hitless in 10 at-bats.