Phillies general manager Matt Klentak announced late Tuesday afternoon that Altherr would have surgery on Wednesday.
Altherr, 25, was a front-runner to be the starting right fielder on Opening Day.
"We're hopeful he'll be back before the end of the season," Klentak said.
Altherr suffered the injury last Friday when he dove for a ball. He went back to Philadelphia on Sunday and received two opinions, with both doctors recommending surgery. Dr. Randal Culp will perform the operation in Philadelphia.
"It's disappointing, certainly, for a young player who had a lot to prove," Klentak said. "We were certainly excited to watch him play. But we're not going to sit here and feel sorry for ourselves. We have a lot of good players in camp that are competing really hard for an opportunity."
Altherr hit .241 with five home runs and 11 doubles in 39 games with the Phillies at the end of last season.
To fill Altherr's void, Klentak said the Phillies will turn to several of the players competing for jobs in camp. Among them are Cody Asche, who shifted from third base to the outfield last May; Darnell Sweeney; Rule 5 pick Tyler Goeddel; and non-rosters players Cedric Hunter and David Lough.
"We owe it to the guys in camp to give them that chance to fill that spot," Klentak said. "We'll survey the market. If there's something out there, we'll explore it. But we feel pretty good about the guys we have here."