Dr. James Andrews operated on the 26-year-old right-hander Tuesday in an arthroscopic procedure in which he also worked on Prior's rotator cuff.
"Dr. Andrews feels comfortable that he will still have a career. This is certainly not career-ending," Cubs general manager Jim Hendry said Wednesday. "He felt optimistic that he would be able to pitch next year. ... At his age, he should not have a problem responding and coming back after a strenuous rehab."
Prior has been beset by injuries since his first full season in the majors in 2003. He went on the disabled list three times last year and started this season at Triple-A Iowa.
"It's best for him. He had some physical problems and now they've been taken care of. I don't think he was going to be able to pitch this way," Cubs manager Lou Piniella said after Wednesday's 9-3 win over the Brewers.
"In a way, I'm happy for the guy because he'll get well now and get strong and he can resume his career without the problems that he had. A lot of pitchers have this type of surgery and bounce back and have very productive careers. So let's hope that's the same in Mark's case."
The injury was the latest problem for the struggling team. The Cubs, who have not reached the World Series since 1945, made many major changes in the offseason. After beating Milwaukee they were 8-13 and last in the NL Central.
Kerry Wood, who teamed with Prior to nearly pitch the Cubs to the NL pennant in 2003, is back on the disabled list with tendinitis in his right shoulder. Wood has not pitched since a spring training appearance March 25, when his arm felt weak and then stiffened up the next day, and Hendry said Wood might resume throwing this week.
According to a team statement, Andrews performed a debridement of Prior's rotator cuff and repaired labral and capsular injuries in the shoulder.
"It stayed in the arthroscopic stage. But I think he had some touch up work in a lot of places," Hendry said. "But at the same time there didn't seem to be anything so significant that it would require more than the scope. It didn't have to be opened up and have extensive surgery."
The Cubs were hoping Prior could rebound this season and compete for their fifth starter's spot that eventually went to Wade Miller. On the day after he was optioned to the minors late in spring training, Prior was convinced he could still get major league hitters out.
"You don't know where your crossroads in your career are until probably after your career is done," he said at the time.
Prior had hoped to start the season with the Cubs.
"There's no reason to ever think that he didn't want to pitch. He was certainly disappointed when he didn't make the ballclub this year and felt like he was good enough to make it," Hendry said.
"He wasn't quite his old self, but he felt that he was on the way. There were no complaints in spring training at all about discomfort or sharp pain. He certainly wouldn't have been pitching if he had."
Prior is 42-29 with a 3.51 ERA in the majors. He took a slight pay cut this season, from $3.65 million to $3,575,000.
Prior finished third in NL Cy Young Award voting in 2003, when he was 18-6 with a 2.43 ERA and struck out 245 in 211 1/3 innings. That October, he was on the mound for Game 6 of the NL Championship Series against Florida with the Cubs leading the series 3-2.
Chicago held a three-run lead in the eighth inning before the Marlins, helped by fan interference on a foul ball at Wrigley Field, rallied to win. Florida also won Game 7 and then won the World Series.