Roger Prinzen's side have lost six games in a row and face Schalke on Saturday as they seek to overhaul Hamburg and give themselves a chance of staying up via the relegation play-off.
Bundesliga ever-presents Hamburg, who are one point ahead of Nuremberg, head to Mainz.
But Prinzen's charges must cope without their first-choice goalkeeper, who has not missed a league game this term.
"Raphael Schafer has suffered a severe muscle injury in his left shoulder and thus will miss tomorrow at Schalke," the club posted on Twitter on Friday.
The 35-year-old is likely to be replaced by Patrick Rakovsky, who has been his understudy throughout the season and played 45 minutes in the 2-0 defeat to Werder Bremen in March.
He becomes the fourth first-team player to be ruled out of the clash with Javier Pinola, Marvin Plattenhardt and Timothy Chandler all serving suspensions.
