Manager Rob Thomson did not offer a timetable for Harper's return.
"It's tough, but it's probably the best thing for him. So whatever's best for him is best for me," Thomson said Tuesday. "If he's able to come back, which we plan on, then that's good under the circumstances."
Harper's thumb was broken when he was hit by a 97 mph pitch from San Diego Padres left-hander Blake Snell on Saturday night.
The 29-year-old Harper is hitting .318 with 15 home runs, 48 RBIs and a .985 OPS, and has helped the Phillies recently surge back into playoff contention.
The Phillies opened a three-game series Tuesday night against Atlanta.
"I've got to be positive for the guys in here. I know they'll pick up the slack. I'm just really bummed for the organization, the guys, the city of Philadelphia, the fans. I love running out there and playing every day. Definitely bummed," Harper said after the injury.
Harper checked his swing as the pitch rode inside and high toward his shoulder before hitting him on the outside of the left hand in the fourth inning. He fell to the ground and was in pain as he held his hand while on his knees for several minutes.
"I think this is probably what's best for him although it's a broken bone and that's bad; he's not happy about that, not being able to play because he wants to play," Thomson said. "But he's looking forward to getting back (near) the end of the year."