Eaton was making his first start since suffering a bruised right knee when he was hit by a pitch Wednesday in a game against Baltimore. He walked as a pinch-hitter Friday against Miami in his only appearance in the interim, then lined out in his only plate appearance Monday.
Gerardo Parra took over in right field after Eaton left the game after the second inning.
Eaton is hitting .288 with 12 homers, 42 RBIs and 13 stolen bases in 128 games for Washington. He played in a combined 118 games in his first two seasons with the Nationals.
The Associated Press contributed to this report.