General manager Dale Tallon told the media of the decision ahead of Florida's 6-5 shootout win over Buffalo.
Jovanovski, 36, had attempted to play through the pain. But he managed to dress for just six games in his second season back with the club he broke into the league with in 1995.
"Obviously, it’s Jovo’s decision," said Tallon. "He’s the one that has to make the final call on that. Nobody knows his body better than he does.
The surgery will be performed next week.
Jovanovski has scored 136 goals and 359 assists for 495 points in 1,091 career regular season games, with lengthy stays with Vancouver and Phoenix. He's racked up 1,452 penalty minutes, fourth among all active players.
The decision sees Jovanovski join Sean Bergenheim, Stephen Weiss and Kris Versteeg as Panthers lost for the season due to injury.