Harper went down to the dirt Friday after being struck by a 96 mph fastball from Toronto rookie Trent Thornton.
Harper stayed on the ground for a few moments, was checked by a trainer and limped off and out of the game in the sixth inning.
Recently signed to a record $330 million, 13-year contract, Harper was playing his fourth exhibition for Philadelphia. The slugging outfielder is 0 for 5 in 10 plate appearances.
Harper had hoped to play three straight games starting Friday.