Eustace went under the knife in January and recently underwent a second “clean up” operation.
However, the 35-year-old, who last played for the Rams in a 1-0 win against Ipswich on January 10, is looking at around another three months on the sidelines.
“We are looking at a rehab period of probably 12 weeks,” Derby first-team coach Paul Simpson told local reporters on Monday afternoon.
“We do not expect John to be available again this season, unfortunately.”
Meanwhile, some good news on the injury front for the Rams is that George Thorne and Jake Buxton could be available for the final league game of the season against Reading at the iPro Stadium.
Thorne has missed the last two matches due to a recurrence of a thigh problem that ruled him out for six games. Injuries have restricted the midfielder to just three appearances this season.
Centre-half Buxton had back surgery recently and has sat out the last seven games.
“George and Jake could be fit for Reading but that is a real fingers crossed and if everything goes to plan,” said Simpson.