The injury, however, will not require surgery. And the 30-year-old will now have plenty of time to rest in anticipation of 2013.
"Great year," Miami manager Ozzie Guillen said of the outfielder. "Nobody can take that away from him."
The Marlins acquired Ruggiano from the Astros in a Minor League trade in late May. He became a regular player, and one of the better stories in an otherwise rough season.
Ruggiano appeared in 91 games and hit .313 with 13 homers and 36 RBIs. He suffered the shoulder injury on Sept. 21 while making a diving attempt on a triple by New York's Scott Hairston.
Ruggiano is under club control, and next year he will get a chance to either win a starting outfield spot or make the roster as a reserve.
"In Spring Training, it will depend what the organization wants to do," Guillen said. "How we're going to use him next year.
"He is one of the very small bright spots this year. We don't have many bright spots. Ruggiano was one of the bright spots that we had."