The 35-year-old has not featured for Fulham since the FA Cup defeat to Sheffield United last month with a knee injury.
Magath has admitted the injury is more serious than they thought and that the Irishman is set to be ruled out for the Premier League run-in as Fulham look to climb out of the bottom three.
"Damien's injury is worse (than we thought). We have to expect that he will not play any more this season," said Magath.
"The problem is his knee - an injury from three weeks ago which he had before I arrived here - and maybe he needs an operation."
The news is a blow for Duff as he now faces an uncertain future with his contract at Craven Cottage coming to an end in the summer.