Scherzer looked sharp on the mound, with his fastball clocked as high as 96 mph, but he lasted just five innings and 67 pitches, departing with the score tied 1-1. The Nats went on to win 7-1.
Scherzer said afterward that it was a "precautionary move," given the left oblique strain that caused him to land on the injured list earlier this season.
"It wasn't anything specific," Scherzer said. "I don't have a strain, it's just the left side was getting tired a lot quicker than usual.
"Was there a scenario where I could pitched the sixth and be OK? Yeah, that could've happened. But if I went out there in the sixth and I got hurt, there's no way I could come in here and look the guys in the face and say that I made the right decision. Better to be safe than sorry in this scenario."
Mets manager Buck Showalter said the team is hopeful Scherzer will make his next start.
"He probably could've continued to pitch, but we didn't think it was a good idea," Showalter said.
"He didn't ask to come out. You know Max is never going to do that. ... Just didn't think it was a good idea to push it."
Scherzer retired the side in order in the fifth, getting Ildemaro Vargas to tap the ball back to him for an inning-ending groundout. Upon entering the Mets' dugout, he was seen walking down the tunnel toward the clubhouse with a team trainer following closely behind him.
Scherzer, who was replaced by Tommy Hunter to start the sixth, allowed one run on three hits with five strikeouts and one walk.