Cloyd (1-0), making his second start of the season, yielded two runs on eight hits while walking two and striking out five.
The right-hander, seeking to replace the injured Roy Halladay in the Phillies' starting rotation, was coming off a 6 1/3-inning, two-run performance in his May 10 debut.
Howard sparked a four-run seventh inning with a two-run single and added another RBI hit in the eighth while Delmon Young went 2-for-4 with a solo homer for the Phils, who evened their three-game series.
Miami's Duane Below (0-1) absorbed the loss after starter Jose Fernandez had tossed five innings of one-run ball.
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