Harper missed four games with a left thumb injury, when he jammed the finger while sliding into third base on Sunday against the Pirates.
Despite the four strikeouts on Friday, Harper said his thumb was not bothering him.
"I felt great tonight," Harper said. I felt really good. And even with the four strikeouts, it happens. I missed some pitches I should've drove, but I felt great."
Baker said before the game that Harper might have been ready to play on Thursday but benefited from an extra day off.
"If a guy tells me he's ready, if I have the luxury, I like to give him one more day off," Baker said before the game. "A lot of guys say they're ready, and then you bring them back, and they're really not ready."
Baker said during his playing career he rushed back from a similar injury and ended up making it worse. To avoid repeating that situation with Harper, the manager took matters into his own hands.
"I went up to him and I pinched his thumb a couple days ago," Baker said, smiling. "And he said, 'Ow, what'd you do that for?' And I said, 'OK, I got my answer.'"
A year after winning the National League MVP Award, Harper entered Friday batting .244 with a .819 OPS and 24 home runs in 144 games this season.
Chris Heisey is currently not with the Nationals because his wife, Lisa, delivered the couple's second child. Heisey is expected to rejoin the Nats on Saturday, according to Baker.
Ryan Zimmerman, Danny Espinosa and Gio Gonzalez were on paternity leave earlier in the season.
Alex Putterman is a reporter for MLB.com based in Washington.