"You're not out of it until 27 outs," said Howard, who was mobbed by his teammates near first base after the hit. "It was a little hectic but, you know what? I'll take it."
Utley singled, tripled, homered and drove in three runs for the Phillies, who snapped a five-game skid against the Mets.
The Mets appeared positioned for their 12th victory in the last 13 games against the Phillies in Philadelphia before the ninth.
Cody Asche led off with a double off Jenrry Mejia (5-5) and scored when Byrd lined a hit up the middle. Two outs later, Byrd stole second and, after getting the count to 3-2, the Mets intentionally walked Utley.
Howard followed with a single to right on a full-count pitch.
The beleaguered slugger, who recently was benched for three games, pointed skyward after rounding first before getting mobbed by his teammates near first base.
"That's big for his confidence," said Philadelphia manager Ryne Sandberg, who benched a slumping Howard for three days in late July. "He's been in these situations before. Right guy in the right place."
Ken Giles (1-0) pitched a scoreless ninth to cap four innings of scoreless relief by three Phillies bullpen arms.
It was the second time in six games Howard faced the scenario. The Astros walked Utley for Howard on Tuesday and the Philadelphia slugger singled home the winning run in Philadelphia's 2-1, 15-inning victory.
"I wasn't surprised at all," Howard said. "The winning run on second base and I didn't have any hits. I still have great confidence. I feel real good about my swing."
While Howard wasn't surprised, Mejia was.
"I want to finish (against Utley) but I'm not the manager," Mejia said. "I have to do whatever the manager wants me to do. A little bit surprised but I can't do anything. Terry Collins is the manager. I'm just the player. I have to do whatever he wants me to do."
Collins stood by his decision.
"I'm not going to let (Utley) beat me," he said. "Howard's been struggling. You've got to make him beat you. In my book, that's the way I look at it."
Zack Wheeler allowed three runs on three hits in six innings. He is 4-0 with a 1.94 ERA in his last eight games.
Kyle Kendrick extended his struggles this season. The right-hander was charged with six runs -- five earned -- on 10 hits in five innings.
"He struggled with balls over the plate," Sandberg said.
Phillies: Prized prospect Jesse Biddle makes his second start for Class-A Clearwater on Monday since being shut down for a mental break on June 23. The 2010 Phillies first-round pick tossed five no-hit innings to earn the victory in Clearwater's 4-0 win last Wednesday against Daytona.
Mets: Rookie right-hander Jacob deGrom will be evaluated in New York on Monday after experiencing shoulder soreness in the days following Thursday's start against Washington. DeGrom, who is 6-5 with a 2.87 ERA in 16 starts, will not make his scheduled start on Tuesday against the Nationals. ... Mejia revealed after the game that he has been struggling with a hernia problem for the last three weeks. "Doctors say if it bothers me too much to let him fix it, but I don't want to let him know because I want to keep pitching," Mejia said.
The teams close out the four-game series at 1:05 p.m. Monday when Phillies right-hander David Buchanan (6-5, 4.39) faces New York lefty Jonathon Niese (5-8, 3.51). Buchanan is filling in for injured lefty Cliff Lee, who is out for the season with an elbow strain. Niese has lost four straight games.
Mets left-handed reliever Josh Edgin struck out all four batters he faced. Edgin is 1-0 with a 1.64 ERA with 19 strikeouts and three walks in 22 innings.
"He's done a nice job," Collins said. "He got us to the ninth inning with the lead, which is what you want."
After David Wright opened the third with a single and Duda flew out, d'Arnaud lifted a medium fly to left field that Brown appeared to pull up on too soon. Fans booed the left fielder, who has experienced offensive and defensive troubles this season.
"It appeared to be catchable," Sandberg said.