Furcal made the decision after visiting Dr. James Andrews' clinic in Pensacola, Fla., on Wednesday.
"It's very disappointing," Furcal said. "I worked so hard in the offseason to get everything straight, working hard with the doctors the training team we did anything we could do to get ready for spring training, ready for the season."
Furcal strained the elbow ligament near the end of last season, keeping him out of the final few weeks and the Cardinals' playoff run. There was a concern then that he would have to undergo offseason Tommy John surgery, but Furcal chose to try rehab instead.
When healthy, Furcal has one of the strongest arms among major-league shortstops. He did participate in some Cardinals fielding drills during spring training, but never threw at 100 percent.
A bone spur in his elbow complicated Furcal's rehab. He expects the bone spur will be removed at the same time he undergoes the Tommy John surgery. An appointment for the operation by Andrews is not yet scheduled but Furcal and the club believe it will happen next week.
"I feel for him just knowing that it's not something that he obviously wanted to go through," St. Louis manager Mike Matheny said. "He tried to do everything he could to stay away from this alternative Now we just hope everything goes well and he gets back as quick as he can."
Furcal said he was given the option of continuing to rehab the elbow for a couple months, but there was no guarantee that choice would get him back on the field for the 2013 season.
"It's tough to decide to get surgery," said Furcal, a 13-year veteran who hit .264 in 121 games for the Cardinals last season, batting primarily in the leadoff spot. "For me it's a very tough situation because I want to keep playing."
That Furcal requires season-ending surgery did not completely surprise the Cardinals.
"I think going into this we always knew this was a plausible outcome," St. Louis general manager John Mozeliak said.
When Furcal went down last season, Kozma took over for the stretch run. After hitting only .232 at Triple-A Memphis, the former first-round pick responded with a .333 average in 26 games and performed solidly in the field. His average dipped to .214 in the playoffs.
St. Louis also signed eight-year veteran Cedeno, most recently with the Mets, to a one-year deal as insurance in case Furcal was unable to play. Daniel Descalso also has the ability to play shortstop.
"The way we look at it right now it is certainly going to be a competition between Kozma and Cedeno but there's no doubt that given what Kozma did for us in the last six weeks of the season last year that we do have a high level on confidence that he can continue to do that," Mozeliak said.
Furcal does intend to continue his baseball career following the surgery.
"I feel like I can still. I am 35 years old. I've seen guys play through 50," Furcal said. "I wanted to get strong and get ready for next year."