The team announced Syndergaard has "a possible lat strain'' and was headed to New York for an MRI secheduled for Monday morning.
Syndergaard allowed five runs on five hits in the first inning and walked his first two batters of the season, one intentionally. He threw 38 pitches before leaving the game, which the Nationals won handily via a 23-5 rout.
An agitated Terry Collins erupted after the game when a reporter prefaced a question by saying he looked upset in the dugout after Syndergaard departed.
"You think?" Collins snapped. "What do you think?"
Syndergaard was scratched from a start Thursday with biceps and shoulder discomfort. He had been scheduled for an MRI on Friday but declined to have one after throwing a bullpen session.
"I think I know my body best," Syndergaard told reporters Friday. "I'm pretty in tune with my body, and that's exactly why I refused to take the MRI."
Syndergaard was not available to reporters in the clubhouse after Sunday's game.
Mets general manager Sandy Alderson said it was unusual for a player to refuse an MRI, but the team couldn't force him to undergo the exam.
"The recommendation was made by the doctor; it was precautionary. He felt strongly that he was fine,'' Alderson said. "We made sure that he threw again before he went out, so we could confirm that, and that's what happened.
"Would the MRI have disclosed a lat issue or reaffirmed some concern about the biceps? We'll never know.''
Alderson said he spoke to Syndergaard after the game, but could not say whether he regretted refusing the earlier MRI.
"We didn't get into that,'' Alderson said. "I didn't think that was necessary at that particular time, so I think he understands now that there's something going on that needs to be examined.''
It was an exasperating and discouraging turn of events for the injury-plagued Mets (10-14), now missing perhaps their two top players. They put star slugger Yoenis Cespedes on the disabled list Friday with a strained left hamstring, one day after he got hurt legging out a double against Atlanta.
First baseman Lucas Duda (hyperextended left elbow) and part-time infielder Wilmer Flores (right knee infection) also are sidelined. Duda had a setback over the weekend during his minor league rehab assignment and won't be activated Monday, when he's eligible to come off the 10-day DL.
Nationals manager Dusty Baker, whose team set a franchise record for runs, said he noticed something about Syndergaard in the first inning.
"We could tell something was wrong,'' Baker said. "He was throwing the ball firm but it wasn't moving like usual. When you have a guy like that, you certainly have to jump on him.''
The Nationals sent 10 batters to the plate in the first, getting five hits and two walks, one intentional.
"When you've got eight days' rest you feel stronger and you want to overpower,'' Mets catcher Rene Rivera said. "He was leaving the ball in the middle.''
Rivera didn't notice anything wrong until the final pitch.
"Noah was grabbing, I guess his lat, and I ran out there and he didn't speak,'' the catcher said.
The Associated Press contributed to this report.