Harper went 0-for-4 with a walk in the team's 3-1 win.
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.
Harper was originally hurt on Tuesday crashing into the wall trying to catch a home run hit by Braves pitcher Tim Hudson.
Nationals right fielder Jayson Werth returned to the lineup after missing two straight games with a strained right hamstring and a bruised left ankle. He went 0-for-2 before being removed in the fifth inning.
Information from The Associated Press was used in this report.