Wagner has been sidelined since Aug. 3 because of a tender pitching elbow. He has tried several times to work his way back, but hasn't been able to shake the pain.
Wearing a protective sleeve on his left elbow, Wagner tested his arm Sunday with disappointing results. Between games of a day-night doubleheader against Philadelphia, he went to the mound in a virtually empty Shea Stadium and faced teammate Gustavo Molina.
A wild Wagner hit the reserve catcher on the left foot with his 13th pitch and walked off the field to consult with a trainer and the Mets' coaching staff. The left-hander will be re-examined by a doctor Monday and is likely done for the season, manager Jerry Manuel said after his team's 6-3 victory in the nightcap.
"It's bittersweet," Manuel said. "Bitter in the sense that we lost Billy Wagner probably for the remainder of the year."
The 37-year-old Wagner is 0-1 with a 2.30 ERA and 27 saves in 34 chances. He is in the third season of a four-year, $43 million contract and ranks sixth on the career saves list with 385.
"He was trying to get us to activate him today," Mets general manager Omar Minaya said. "The last pitch he threw, he really felt some discomfort in the elbow area. He didn't want to risk it. ... We are going to be conservative."
New York leads the second-place Phillies by two games with 19 to play. Surprisingly, the Mets are 22-11 since Wagner went down.
"Hopefully, he can bounce back. But if he doesn't, obviously it's a tough loss," New York slugger Carlos Delgado said. "Good teams are able to overcome injuries."
Luis Ayala, acquired from Washington last month in a trade, has quickly become Manuel's closer. Ayala, who struggled with the Nationals most of the season, is 5-for-6 in save opportunities for the Mets.
Ayala allowed an unearned run in the ninth Sunday night. Before that, Mets relievers had not allowed a run in 23 innings since Aug. 31.
Still, Wagner's loss is a huge one for a bullpen that has been unreliable much of the year. Manuel has mixed and matched as much as possible with his relievers during the past month.
"Anytime you have a guy such as him and you lose him, it becomes a big challenge," Manuel said. "I think they have matured somewhat down there very well. We have some candidates down there to get outs. We just have to continue matching them up."