Cole Hamels (2-11) blew a 3-0 lead in another disappointing outing for the three-time All-Star. He allowed four runs and seven hits in six innings.
"It's been a bad case of not keeping the team in games," Hamels said.
The Phillies have lost two in a row after coming within one out of sweeping the defending NL East champion Washington Nationals before Jonathan Papelbon blew a save Wednesday night. They're four games under .500 and just four games ahead of the Mets.
Hamels didn't allow a hit until Young lined a double off the wall to start the fourth. One out later, David Wright's RBI single cut the deficit to 3-1.
Young hit a two-run single with two outs in the fifth to tie it at 3. Lagares doubled and Omar Quintanilla singled before Young's key hit.
"I just tried to take a nice swing, not put pressure on myself and put the barrel on it," Young said.
After Lucas Duda walked in the sixth, Lagares ripped a two-out RBI double to left-center to make it 4-3. Lagares finished 3 for 4 with two doubles.
"That was a great win for us," Mets manager Terry Collins said. "Down 3-0 to Cole Hamels, this is big."
Hefner allowed one earned run in each of his previous three starts without getting a win. This time, he earned his first win since May 29.
The Phillies gave Hamels a 3-0 lead in the second. Ryan Howard led off with a double to right-center and scored on Domonic Brown's double down the right-field line. After Delmon Young singled, Brown scored on a grounder by Ben Revere.
Hamels hasn't received much run support this season, contributing to his poor record. But he has an 8.63 ERA in the eight starts in which the Phillies have scored at least three runs for him. He's 2-5 with a no-decision in those games.
"He wasn't real sharp," Phillies manager Charlie Manuel said. "I've seen him better. He got hurt with two-out hits."
The Mets placed LHP Jonathon Niese on the disabled list because of a partial tear in his rotator cuff. RHP Greg Burke was called up to take his spot. ... The Phillies sent INF Michael Martinez to Triple-A Lehigh Valley to make room for Chase Utley, who came off the disabled list. ... Hamels fell to 6-11 vs. the Mets. ... Parnell has saved nine of his last 10 chances. ... Revere extended his hitting streak to 11 games with a bunt single. ... Dillon Gee (5-7) faces Phillies rookie Jonathan Pettibone (3-3) on Saturday.
40,062 (91.8% full) - % is based on regular season capacity
81 degrees, partly cloudy
Home Plate - D.J. Reyburn, First Base - Bill Welke, Second Base - Adrian Johnson, Third Base - Fieldin Culbreth
From Elias: Cole Hamels fell to 2-11, tying his career high for losses in a season. It's the most losses for a Phillies pitcher before the end of June since 1937.
That year, Wayne LaMaster AND Claude Passeau did it for a team that finished 31 games under .500. Hamels still has one more start scheduled this month.