Utley was a late scratch with a rib injury suffered during batting practice. Phillies manager Charlie Manuel said the second baseman would be evaluated on Wednesday.
"When he took a swing, he kind of felt a burn, a pain, in his rib cage," Manuel said.
Also before the game, Philadelphia placed catcher Carlos Ruiz (strained hamstring) on the 15-day disabled list.
Young, meanwhile, had two hits to raise his average to .214 after returning from offseason ankle surgery. Howard returned to the lineup after missing the previous two games with a sore left knee.
"We haven't been scoring many runs and I haven't been contributing like I'm capable of," Young said. "Hopefully we can carry this over to tomorrow and the rest of this road trip because we're going to need to score runs the rest of this road trip to win ballgames."
Manuel said he glad to see Young "click" and homer for the second time this season.
"We think Delmon can hit," Manuel said. "He's 27-years-old, we definitely think he has a lot of baseball left in him. It's just a matter of him getting some at-bats and getting going."
Howard said he felt good two days after getting a cortisone shot on his left knee.
"It felt better. I'll just continue to try and build on it," Howard said. "I saw the ball pretty well and was able to get a couple of knocks off two lefties. Really, I was just focused on putting together good at-bats."
Tyler Cloyd (1-0) allowed two runs and eight hits in seven innings. He was recalled from Triple-A Lehigh Valley (International League) earlier in the day.
"Up here, I'm definitely keeping the ball down more than I did at Triple-A," Cloyd said. "I think I try to do too much down there and get out of my game at certain times."
Miami's Jose Fernandez went five innings, allowing one run and five hits. He walked one and struck out two.
"Every time I can go out there and give the team a chance to win and a chance to stay in the ball game, I'm happy," Fernandez said.
Howard's single with the bases loaded scored two runs and highlighted a four-run seventh that gave the Phillies a 6-1 lead. He received a cortisone shot Sunday.
Young's ground out and Brown's double scored the other Phillies runs in the seventh. Young homered to left-center on a 2-2 pitch with one out in the fourth. It was his second home run of the season.
Juan Pierre's seventh-inning RBI single pulled Miami within 6-2.
Howard added an RBI single in the eighth off Wade LeBlanc.
Miami's Justin Ruggiano had a run-scoring double with two outs in the ninth.
Pinch-hitter Jordan Brown's sacrifice fly in the fifth scored Placido Polanco to tie it at 1 and take Fernandez off the hook.
- The crowd of 13,996 was the third-smallest at Marlins Park this season.
- Marlins RHP Kevin Slowey (1-4, 3.44) opposes LHP Cliff Lee (4-2, 2.83) in the series finale on Wednesday night.
- Marlins manager Mike Redmond said injured RHP Nathan Eovaldi (shoulder) was scheduled to throw a bullpen session on Wednesday before 60-65 pitches in a start with Class A Jupiter (Florida State League) on Saturday.
- Miami's Chris Coghlan tripled for the second straight game after going 121 games without one.