Recovery for this type of surgery is typically three months.
"The prognosis is that he's going to be fine for next year," Phillies interim manager Pete Mackanin said.
The Phillies selected the contract of infielder Chase d'Arnaud to give the Phillies additional infield depth.
Hernandez hit .272 (110-for-405) with 20 doubles, four triples, one home run, 35 RBIs, 19 stolen bases and a .687 OPS in 127 games. His OPS ranks 17th out of 21 qualified second basemen in baseball.
He showed some potential this season and he is expected to be the team's Opening Day second baseman in 2016. Darnell Sweeney and Andres Blanco are expected to see the majority of playing time at second with Hernandez out.
"I've seen enough that I'd feel comfortable with him at second base," Mackanin said about Hernandez. "It doesn't mean that anything else could come up, trades, anything like that could happen. But I like him. He offers a lot. He can steal a base. This is his first year getting this many at-bats at this level, so I think he's learned from it. He's learned from some of the mistakes that he made. We all do. I like what I see."
Todd Zolecki is a reporter for MLB.com. Read his Phillies blog The Zo Zone, follow him on Twitter and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.