A Wednesday morning MRI revealed the damage.
Eischen, 36, will miss the rest of the 2006 season and the damage could be career-threatening. He had been pitching in pain all season.
In his latest outing Monday night at Philadelphia, he threw to only two batters in the seventh inning before leaving with shoulder pain.
"It didn't make any sense that I couldn't throw strikes," Eischen told MLB.com. "I realized that I was hurting the team."
"I figure something like this would take at least a year to a year and a half to come back," said Manager Frank Robinson. "I knew it was hurting him pretty good."
Eischen, a lifetime middle reliever, was 0-1 this season with an ERA of 8.59 in 14 2/3 innings over 22 relief appearances.