Philadelphia won for the fifth time in seven games with Jonathan Pettibone working 6 1/3 innings for the victory.
Howard hit a solo homer in the second and Ben Revere added an RBI single later in the inning. Utley's homer came in the third to give Philadelphia a 3-0 lead.
Domonic Brown produced another Philadelphia home run in the fourth, his fifth of the year and his second in as many nights.
Pettibone (2-0) gave up a run on five hits without a walk. Jonathan Papelbon recorded a 1-2-3 ninth to pick up his fifth save.
The loss, Miami's third straight, went to Ricky Nolasco (2-3). He allowed four runs on eight hits in six innings.
Philadelphia has won 11 of its last 14 meetings with the Marlins.
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