Harper winced on a check swing in the sixth inning of Washington's 2-0 victory on Wednesday and soon left the game.
Harper said he was diagnosed with a bruise under his left shoulder blade. Washington manager Davey Johnson said Harper is taking medication to relieve swelling.
The 20-year star ranks among the top five in the National League in homers, batting average and assists.
Nationals right fielder Jayson Werth returned to the lineup after missing two straight games with a strained right hamstring and a bruised left ankle.