Cliff Floyd deposited the third pitch he saw from reliever Dan Pleasac over the centerfield wall to tie the game at four in the eighth before Tony Clark won it in the ninth with an RBI single off Terry Adams (0-2) into right field that scored Marco Scutaro from second.
"It's been a while since we've been able to celebrate like that," said Mets manager Art Howe to the Associated Press.
Armando Benitez (1-3) pitched a scoreless ninth to pick up the win.
Leading off the bottom of the first, Roberto Alomar hit the first pitch he saw from Phillies' starter Randy Wolf into the right center gap for a double. Jay Bell walked and first basemen Jason Phillips grounded into a double play that plated Alomar and gave the Mets and early one run lead.
Tsuyoshi Shinjo hit his first homer of the year in the third into the Phillies' bullpen and gave the Mets a 2-0 cushion. The centerfielder, who has struggled mightily this season, went 2-for-2 and is now now hitting .203 on the season.
Jim Thome began the Phillies' (26-20) sixth against Al Leiter by singling into centerfield and was followed by consecutive walks from Pat Burrell and Bobby Abreu. David Bell then lined a run scoring hit up the middle and Todd Pratt grounded out to first that knotted the game at two.
Rookie Marlon Byrd drove in the go ahead run with a sacrifice to right field which knocked in Bobby Abreu. Philadelphia took a 4-2 lead in the seventh on an RBI single into left field by Abreu.
Pinch hitter Tony Clark drew a two out bases load walk in the bottom of the seventh to bring the Mets (20-26) within a run before Cliff Floyd tied the game an inning later.
Al Leiter -- coming off a horrendous 4 2/3 inning performance in which gave up 10 runs and 13 hits in San Francisco -- worked six innings and allowed five hits, three runs, and six walks while fanning five.
Randy Wolf went five innings and surrendered four hits, two runs, and one walk while striking out four. The young lefty is 2-2 with a 3.44 ERA in 11 games against the Mets in his five year career.
P Al Leiter came into the game 7-5 with a 4.30 ERA lifetime against the Phillies in 18 games... LF Cliff Floyd now has 20 RBIs in his last 19 games... 1B Mo Vaughn, trying to determine what course of action to take with his inflamed left knee, saw his fifth opinion on Tuesday in Colorado... Vincente Padilla (3-5, 4.23) opposes Pedro Astacio (2-1, 6.75) on Thursday afternoon...