Encarnacion, 32, has not played since Aug. 30, 2007, when he was struck in the face by a foul ball while he stood in the on-deck circle at Busch Stadium. He suffered severe vision impairment as a result of the incident and spent all of 2008 away from the team recuperating.
It is unlikely that the injuries will allow Encarnacion to play again.
"I believe he still has a difficult road ahead," general manager John Mozeliak said. "He was part of a special year here, culminating in the 2006 World Series championship. He was a good teammate, and he understood that being a professional baseball player was very special. We here in St. Louis all wish him the very best."
The other '08 Cardinals who filed for free agency are Braden Looper, Ron Villone, Russ Springer, Jason Isringhausen, Cesar Izturis, Felipe Lopez, Mark Mulder and Jason LaRue. However, LaRue quickly re-signed a one-year deal to return as the Cards' backup catcher.
Teams hold exclusive negotiating rights with their own free agents for 15 days after the World Series ends. That means that the six players can only negotiate with St. Louis until Friday, Nov. 14. They may speak with other teams, but not about contract specifics.
Matthew Leach is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.