Kremchek repaired a significant partial tear of his rotator cuff, as well as a tear and fraying of his posterior labrum.
Pena's arm will be placed in a sling for approximately three weeks, at which time a formal rehab program will begin.
Pena will be out for four to six months, but is expected to be ready for Spring Training.
Pena had been playing with the shoulder injury for over a month, but denied to the media for weeks that he was injured.
It wasn't until last Thursday afternoon that he officially said he had a problem with the shoulder.
Pena was having the worst year of his career, hitting .205 with two home runs and 10 RBIs. He acknowledged that he had a tough time getting around on fastballs because of the shoulder.
"Last year, I was killing all those fastballs," he said. "This year, I would pop it up."
Bill Ladson is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.