Ryan Madson (2-1) pitched a scoreless ninth and Brad Lidge worked out of a bases-loaded situation in the 10th to earn his fourth save in five opportunities.
Jorge Cantu and Dan Uggla homered on consecutive pitches for Florida, which blew a ninth-inning lead for the second straight night.
Howard and pitcher Chan Ho Park connected for the Phillies. Park's homer was his first since 2000.
Florida led 4-3 before Philadelphia tied it in the ninth on pinch-hitter Eric Bruntlett's run-scoring groundout.
Chris Volstad allowed three runs, two earned, and four hits in seven innings for Florida. He struck out six, walked one and hit a batter with a pitch.
The Marlins scored four times in the fourth to erase a 2-0 deficit. Cantu hit a three-run shot and Uggla went deep on Park's next pitch.
Park gave up four runs and five hits in seven innings. He retired the last eight batters he faced.
Park went deep with one out in the third to give the Phillies a 1-0 lead. It was Park's third career homer and first since Sept. 29, 2000, for the Los Angeles Dodgers off Woody Williams at San Diego.
Florida closer Matt Lindstrom was unavailable one night after throwing 38 pitches and surrendering a career-high seven runs. Notes: Phillies LHP Cole Hamels threw before the game and remained on schedule to start Tuesday against Washington. ... Cantu returned to the lineup after missing three games with a sore wrist. ... Florida manager Fredi Gonzalez said he would name Sunday's starting pitcher following Saturday night's game. ... Phillies manager Charlie Manuel was ejected by plate umpire Ed Montague with two out in the bottom of the 10th for arguing balls and strikes.
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