Rookie right-hander Tyler Cloyd (2-1) pitched eight innings of three-hit ball and the Phillies stayed four games behind St. Louis for the second NL wild card, with two other teams in their path. The Phillies and Cardinals both have 12 games left.
Juan Pierre matched a career high with five hits, Utley added four and Philadelphia set season highs for runs and hits (21) - including 19 singles. Utley had four RBIs, and his double in the sixth was the only extra-base hit until Howard hit his 12th career slam in the ninth.
Boosted by their biggest inning of the year, the resurgent Phillies finished a three-game sweep and won for the 11th time in 14 games.
New York rookie starter Jeremy Hefner (2-7) did not record an out in the makeup game for Tuesday night's rainout. With the Mets setting marks for futility at home, it appeared fewer than 1,000 fans were in the stands for the first pitch.
The announced "crowd" was 20,010, the smallest at 4-year-old Citi Field - and those who were there watched the Mets get overwhelmed right from get-go.
New York, which has dropped five straight and 11 of 12, allowed nine first-inning hits for the first time in its 51-season history. The Mets lost their ninth consecutive home game for the second time this summer and fell to 4-25 in their last 29 at Citi Field.
The previous team to win only four times in a span of 29 home games was the 1980 California Angels, according to STATS LLC.
Mike Baxter homered on an 0-2 pitch but New York has gone a club-record 16 straight home games without scoring more than three runs. STATS said the only other team since 1949 with a streak so sluggish at home was the 2010 Seattle Mariners, who also went 16 in a row.
Utley hit a pair of run-scoring singles in the 33-minute first. Rollins got it started with a bloop single, then added a two-run single and scored twice in the inning. He finished with three RBIs.
Pierre also had two hits in the first, including a bunt single, with Mets manager Terry Collins visibly steaming in the dugout.
Hefner, starting for the first time in 12 days, gave up six straight singles and then a walk to begin the game. Two were bloopers, plus Pierre's perfect bunt.
Howard connected off rookie left-hander Josh Edgin, who gave up a go-ahead homer to the big slugger in Philadelphia's 3-2 victory Wednesday night.
New York used 10 pitchers in the game and needed 58 pitches to get through the first inning.
Mets left fielder Lucas Duda threw out a runner at the plate in the fifth.
NOTES: Phillies C Carlos Ruiz was rested but probably will catch RHP Kyle Kendrick on Friday night against Atlanta, manager Charlie Manuel said. ... Philadelphia finished 8-10 against the Mets this year. ... Mets RHP R.A. Dickey (18-6) will pitch on regular rest Saturday against Miami instead of Sunday. RHP Chris Young (4-8) was pushed back a day to Sunday. The move was made so Dickey can start New York's final home game of the season next Thursday against Pittsburgh - perhaps trying for his 20th win. He also avoids facing Atlanta again after compiling an 8.80 ERA in three starts against the Braves this season. ... Fred Lewis played right field for the Mets in his first major league start since Aug. 30, 2011. ... Baxter made his first start in center field. ... It was New York's smallest crowd since 19,557 showed up at Shea Stadium on April 5, 2006, according to STATS.