He left Nationals Park to get a precautionary MRI on the hamstring, according to a team spokesperson.
"We took him out for precaution," Washington manager Dusty Baker said after his team's 4-1 loss to the Pittsburgh Pirates. "We gotta make it to the playoffs healthy. So we thought it was better that we make that move, the precautionary move, to get him ready.''
Baker downplayed the severity of the injury, but with six days until Washington opens an NL Division Series at home against the Chicago Cubs, the team did not want to take any chances with its NL Cy Young Award contender.
"In a bigger situation, he probably could have stayed in the game,'' Baker said.
Scherzer, who leads the league in strikeouts and is 16-6 with a 2.51 ERA, stumbled on a 2-2 pitch to Josh Bell in the fourth inning, briefly jumped around the mound and bent over.
Scherzer then began to throw a full-count pitch but abruptly stopped when time was called.
Baker, pitching coach Mike Maddux and team trainers visited the mound and quickly took Scherzer out.
Scherzer had given up one hit and struck out five (raising his season total to 268) in 3⅓ scoreless innings when he was hurt.
"[Scherzer] threw a pitch, and I didn't know if he slipped on the dirt. It looked awkward," Nationals first baseman Ryan Zimmerman said. "So I went up there and asked him, 'Are you all right?' And he said, 'Yeah. I'm fine. I'm fine. I'm fine.' And came out and talked to the trainers. There's really no point in doing anything right now. But he said, 'Yeah, I'm fine.' I guess we'll see.''
Scherzer, 33, has now left four of his past 10 starts with various ailments.
The two-time Cy Young winner left an Aug. 1 start at Miami with neck spasms.
On Aug. 19, Scherzer was scratched from a scheduled start against San Diego and placed on the 10-day disabled list with a recurrence of that neck injury. It was his first stint on the DL since 2009.
On Sept. 2, Scherzer took a line drive off his left calf in the first inning of a game at Milwaukee and was pulled after 75 pitches when the muscle tightened at the end of the fifth inning.
"It was time for us to make a decision,'' Baker said. "Max didn't want to come out. We thought it was best. Max never wants to come out. We thought it was best for him and us for him to go out."
The Associated Press contributed to this report.