Jimmy Rollins hit a leadoff home run but the Phillies went into the ninth with only two hits. Chase Utley worked a two-out walk against rookie Josh Edgin (1-2), filling in for ailing Mets closer Frank Francisco, and Howard launched a 93 mph fastball off the facing of the second deck in right field to give his team a 3-2 lead.
The big slugger pumped his fist as he rounded first base and Phillies players broke into a happy frenzy on the bench. It was Howard's 11th homer in an injury-shortened season and first since Aug. 31.
Trying for a last-gasp postseason charge after a miserable first half, the surging Phillies (75-74) won for the 10th time in 13 games. They began the day four games behind St. Louis for the second NL wild-card spot - with three other teams in between.
Cole Hamels equaled a season high with 10 strikeouts over six innings and left trailing 2-1. Philadelphia's young bullpen kept it close, and Jeremy Horst (2-0) got Andres Torres to ground into an inning-ending double play with the bases loaded in the eighth.
Jonathan Papelbon worked a one-hit ninth for his 36th save in 40 tries.
The punchless Mets wasted a splendid outing from Matt Harvey, who finished his rookie season with a flourish. David Wright hit a solo homer but the Mets (66-82) dropped their eighth straight home game and 24th in the last 28 at Citi Field.
This one guaranteed them a fourth consecutive losing season, despite a 46-40 first half.
New York has lost four in a row and 10 of 11 overall. The Mets have managed three runs or fewer in a team-record 15 straight home games since a 6-5 win over Atlanta on Aug. 12 at Citi Field.
The previous major league club to score three runs or fewer in more consecutive home games was Seattle, which went 16 in a row in 2010.
Harvey struck out seven and did not allow a hit after Rollins' home run in the latest eye-catching performance of his promising season. This one was the last, too. The prized right-hander, drafted seventh overall in 2010, will be shut down after 10 major league starts to protect his 24-year-old arm.