Luebke missed all of last season while rehabbing after having his first surgery in May 2012.
An MRI exam last week showed a tear in the ulnar collateral ligament.
He is 10-12 with a 3.25 ERA in parts of three seasons.
Luebke signed a $12 million, four-year contract in 2012. The deal has team options for 2016 and 2017 that could make the contract worth $27.75 million.
Manager Bud Black said it looked like the graft didn't take in Luebke's first surgery.
Had the first operation been a success, the Padres planned to ease Luebke back and would not have had him penciled into the rotation early on.
''Cory would have been a bonus,'' Black said Wednesday. ''I think the world of Cory. I think the world of his ability, his stuff, his heart, his guts. If he had come back, it would have been great. ... You look at the numbers on the Tommy John, there's a 15-20 percent number in there that guys don't come back from that surgery and Cory unfortunately fell into that group.''
Said catcher Nick Hundley: ''It's bad news. Cory's a great guy. It's tough when a guy does everything he can to get back and something goes wrong. It's tough for us as a franchise because he could be the face of the franchise. He's that good, that quality of a guy. You could literally hang your hat on that kind of guy. From that standpoint it's tough, but he's resilient. I was with him when he got the news. You hope for the best for him. If anybody's going to come back, it's Cory Luebke.''
Also Wednesday, left fielder Carlos Quentin said his legs feel much better heading into this spring training than they did at this point last year. He had surgery on his right knee late last season after being limited for a second straight season. It was his third surgery on his right knee in 18 months.
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