The Nationals beat the Braves 2-1 to avoid a three-game sweep.
Harper went 0-for-4 in Saturday's 6-2 loss to Atlanta and has no RBIs in Washington's first five games this season.
"I'm pretty lost right now actually," Harper said after Saturday's game. "I'm trying everything right now so we'll see where I'm at tomorrow, give pops a call and see what he says.''
Nationals third baseman Ryan Zimmerman, who was pulled from Saturday's game with a shoulder injury, and outfielder Denard Span also were out of the starting lineup Sunday. Zimmerman came in to pinch hit for Tyler Clippard in the bottom of the eighth.
An MRI on Zimmerman's shoulder showed inflammation but no structural damage, according to manager Matt Williams.
"It's just sore," Zimmerman said, according to the Washington Post. "It was more sore yesterday than it usually is. The last however many years I've played when it felt good, I've played when it felt bad, and yesterday it felt worse than normal. I thought it was the right thing to tell [Williams] and see what we've got."
Zimmerman committed his second throwing error of the season Saturday night, leading to two unearned runs. He's experienced throwing problems since having shoulder surgery after the 2012 season.
The Nationals also placed outfielder Scott Hairston on the 15-day disabled list Sunday with a strained left oblique.
Hairston says he was hurt while swinging during an at-bat against the New York Mets on Thursday. Replacing Hairston on the roster is first baseman-outfielder Tyler Moore, who was recalled from Triple-A Syracuse.
The Associated Press contributed to this report.