The Dodgers made the announcement on Friday night. They did not say why Scherzer will not start and did not say which pitcher will take his place.
Atlanta leads the series 3-2.
Scratching Scherzer was first reported by the Los Angeles Times.
Scherzer, a 37-year-old right-hander, is a three-time Cy Young Award winner acquired by the Dodgers from Washington on July 30.
He got his first career save on Oct 14 at San Francisco in Game 5 of the Division Series, throwing 13 pitches on two days' rest after throwing 110 pitches over seven innings during the Dodgers' 1-0 loss in Game 3.
Scherzer started Game 2 at the Braves on Sunday and did not get a decision in Atlanta's 5-4 win, throwing 79 pitches over 4 1/3 innings. He said after that game he had a bit of a dead arm but said at the time he did not think it was that big of a deal.
Jorge Castillo of the Los Angeles Times reports Walker Buehler could start on short rest for the second time in the playoffs for the Dodgers or the team could go with a bullpen game -- with Tony Gonsolin or David Price taking the bulk of the innings.
Price was added to the team's roster in place of Joe Kelly, who suffered a season-ending biceps injury in Game 5.