The Phillies ended the Mets' seven-game winning streak and stopped New York's 11-game winning string at Shea Stadium, its best run at home since September 1995.
Philadelphia began the day in third place in the wild-card chase, 2 1/2 games behind Cincinnati and also trailing San Diego.
"That's what the National League is this year," said Phillies manager Charlie Manuel, who was ejected in the sixth inning. "You're looking at those teams jammed in there and there's a reason. It's a lot of teams similar. They've got some weaknesses but they've managed to stay afloat. That's why you see the wild-card race right around .500 baseball."
Carlos Beltran hit his 37th homer, doubled and drove in three runs for the NL East-leading Mets.
Howard drove in three runs, giving him a league-leading 117 RBI. He had a sacrifice fly in the first inning and hit a two-run homer in the third.
In the bottom of the third, Howard came off the bag at first base to make a diving play on Shawn Green's hard grounder with runners at the corners.
That was enough to keep Wolf ahead. He allowed three runs and five hits over five innings while making just his sixth start of the season after having Tommy John surgery in July 2005.
"This year is kind of like a constant work in progress where I'm making adjustments every time out, just trying to get my mechanics in line," Wolf said.
"Physically, I felt really good. The bullpen did a great job today and really all the credit goes to them today," he said.
The Phillies lost closer Tom Gordon two weeks ago to a strained right shoulder, but have excelled without him. Philadelphia's bullpen has a 2.38 ERA over its last nine games.
Rookie Brian Bannister (2-1) lost in his first game for the Mets since injuring his hamstring on April 26. He settled down after a rough start and gave up four runs and six hits in six innings.
"I just got beat by one of the best hitters in the league this year," Bannister said. "I was just debating whether I should throw him a strike in that situation and he got three RBI off me."
Bannister was 2-0 with a 2.89 ERA in five starts for the Mets before hurting himself with running the bases at San Francisco. He re-aggravated the injury three weeks later in a rehab start at Triple-A Norfolk and didn't pitch again until Aug. 5.
"He settled down nicely. A little shaky, but gathered his composure," Mets manager Willie Randolph said. "I was impressed with the way he kept his cool."
Not impressed enough, though, as the Mets optioned Bannister to Triple-A Norfolk after the game. Oliver Perez was called up from Triple-A Norfolk to start Saturday.
In his next at-bat, Howard sent a 3-2 pitch from Bannister to nearly the same spot in right -- but a few feet farther -- and over the wall for a 4-0 lead. Beltran hit his RBI double in the bottom half.
"Playing against these guys you've got to get out early and try to get as many as you can because you never know when they're going to have a little outbreak and score some more runs," Howard said.
- Mets SS Jose Reyes jammed a finger on his left hand while stealing second base in the fifth inning, but stayed in the game.
- The Phillies won three of four from the Mets last week in Philadelphia.