Red Sox manager Terry Francona said Ellsbury was sore and may not be able to play Sunday at Kansas City.
Ellsbury was hit by Royals reliever Everett Teaford in the eighth inning Friday night.
Ellsbury is hitting .313 with 22 home runs, 79 RBI and 33 stolen bases. He was replaced in center field by Darnell McDonald.
Shortstop Marco Scutaro, who had not played since Aug. 13 because of a stiff back, returned to the Boston lineup.