Bay suffered a non-displaced fracture of a rib on his left side while attempting a full-extension catch in Game 2 of Monday's doubleheader, on a deep shot by Gregor Blanco.
Pelfrey, for now, is diagnosed only with right elbow inflammation. Still, general manager Sandy Alderson said ligament damage has not been ruled out, meaning Tommy John surgery could be forthcoming. A major league source, however, said that team officials are aware Pelfrey has a partial tear of the ulnar collateral ligament and team officials are bracing to lose him to season-ending surgery.
"It's frustrating to lose a doubleheader one day and two players the next," Alderson said.
The Mets also had placed backup infielder Ronny Cedeno on the disabled list before Monday's doubleheader with a strained intercostal muscle on his left side.
Pelfrey said he was not convinced ligament damage occurred, and speculated his absence may be limited.
Pelfrey said he felt "tightness" and "grabbing" in his right elbow during the first pitch of every inning Saturday, while limiting San Francisco to one run in eight innings. The sensations quickly would go, but resurface before the next inning.
He went for a precautionary MRI on Tuesday morning at the Hospital for Special Surgery, which revealed a spot, Pelfrey said. Doctors had not made a final diagnosis yet, he said.
"I felt good the other day," Pelfrey said. "I would throw one pitch and it would go away. The ball was coming out good. Everything felt good. There was just a little bit of tightness, which I thought was a little bit of tendinitis."
Alderson said Pelfrey will seek a second opinion, but Pelfrey said nothing had yet been firmly planned.
The Mets would not place a firm timetable on the length of Bay's absence, but the left fielder said the crack in the rib was relatively small. Bay did a face plant into the ground after the ball glanced off his glove while he made a lunging attempt.
Although the Mets announced Monday night that X-rays taken at the stadium were negative, Bay had said he planned more tests for Tuesday morning. Bay did not feel fully comfortable postgame. He described the rib area as "sore" and said he was not breathing normally.
"I knew it hurt pretty well," Bay said. "I was hoping, best case, that it was a bruise. I got up this morning and the way it was feeling, if it was a bruise, it was a pretty good one."
Left-handed reliever Robert Carson has been promoted for the midweek series against the Miami Marlins. He is expected to be replaced by Chris Schwinden for Friday's start at Colorado. Corner infielder Zach Lutz was promoted for Bay.
Lutz primarily will serve as a righty bat for the bench, but manager Terry Collins suggested he likely would use Lutz against left-hander Mark Buehrle on Wednesday at first base over slumping Ike Davis.
Meanwhile, middle infielder Jordany Valdespin -- who first started learning center field during spring training -- now is getting a crash course in left field. Valdespin had been promoted Monday for Cedeno.
Mike Baxter is starting in Bay's position on Tuesday night, but Collins suggested he may liberally use the rookie Valdespin at the position against righty pitching, with Scott Hairston facing southpaws.
Outfielder Andres Torres, who landed on the DL after Opening Day with a strained left calf, is due to rejoin the Mets on Monday in Houston, Alderson said.
Torres began a rehab assignment with Class A St. Lucie on Monday night. Alderson said Torres is set to play again Tuesday and Wednesday with St. Lucie, then play in a cold-weather climate -- either with Triple-A Buffalo or Double-A Binghamton -- on Friday and Saturday before being activated.
Schwinden would be on turn for Friday's start. Alderson ruled out using prospect Matt Harvey or Jeurys Familia.
Jeremy Hefner, who tossed three scoreless innings in Game 1 of Monday's doubleheader before being returned to Triple-A Buffalo, would not be eligible to return because he must spend 10 days in the minors unless he directly is replacing the player who landed on the DL.
The injuries forced Collins to juggle his lineup.
Kirk Nieuwenhuis and Ruben Tejada are now batting in the Nos. 1 and 2 slots, with Daniel Murphy dropping to third. The slumping Davis, once the cleanup hitter, has dropped all the way down to No. 6.