Werth was listed in manager Matt Williams' original lineup in right field for Saturday night's game against the Braves but instead was held out for the second straight game.
Williams said Friday Werth was ''pretty banged up'' and has battled the sore shoulder for more than a week.
The Nationals had no immediate update on Werth's status when they announced the lineup change. Bryce Harper moved from left field to right field. Kevin Frandsen entered the lineup in left field in Williams' revised lineup.
Williams said outfielder Steven Souza was feeling better Saturday after hurting his shoulder Friday night in a collision with the right-field wall.