Heffernan tore a groin muscle in the warm-up before the 2-0 home loss to Aberdeen nearly a fortnight ago, and the severity of the problem means that the 32-year-old will not kick a ball again this season.
Butcher, who also will not be able to call on the defender Paul Hanlon again this term due to a knee problem, said: "Paul Heffernan has suffered a nasty one - he's pulled the muscle away from the bone and won't play again this season."
The loss of Heffernan is a set-back for a Hibernian side that have only won once in their last 14 outings, a run of form that has left the club just four points above second-bottom Partick Thistle ahead of Saturday's trip to St Mirren.
Butcher, however, is hopeful that centre-half Jamie McPake, who has not played since last October after undergoing a back operation, may soon be ready to return.
The manager said: "James came back into training a few weeks ago and he's been looking good. He wants to play before the end of the season."