The official was left with serious injuries, and taken to a local hospital via ambulance for treatment.
One supporter at the game said: "Nobody really saw what happeñed as one of the Stockport players had just taken a dramatic tumble and was getting comedy boos from his own fans.
"Next thing the linesman was on the ground, he stayed down a long time though."
Scunthorpe will play Carlisle in the final on Thursday night.