Harper is likely to need surgery in the near future, and he has battled through the pain barrier with a groin injury for several weeks.
He struggled to take goal-kicks and make clearances, but the Easington-born keeper played on.
Injury Kept Harper Out At Arsenal
Shay Given returned against Arsenal on Saturday but after the game Roeder confirmed Harper's injury ruled him out of the match.
Glenn Roeder: "Steve Harper was unfortunate not to play today. He has done really well for us.
Glenn Roeder: "Steve Harper was unfortunate not to play today. He has done really well for us.
"He has carried an injury for five or six weeks and unfortunately he will probably need some surgery soon."
Tim Krul is also spending time in the treatment room with a knee injury, so veteran Pavel Srnicek is back in the frame as No 2.