The striker will sit out a long spell on the sidelines, after being rushed to hospital following a knee injury sustained against Borussia Dortmund
The 29-year-old, whose goal contributed to the Royal Blues sealing the Ruhr derby, was stretchered off in pain during the second half and taken to a nearby hospital.
Early tests indicated several knee ligaments had been strained, effectively ruling Huntelaar out for the rest of the season, including the crucial tie against Fatih Terim's men in midweek.
The Gelsenkirchen outfit will have to contend without their star during the second leg at the Veltins Arena, with the game finely-poised after a 1-1 stalemate in Istanbul.
"It's very, very unfortunate," Schalke coach Jens Keller told reporters after his side beat Dortmund. "He's in the hospital after an MRI scan, and it looks like a long-term injury."
Keller's men remain in the hunt for Champions League qualification this term as well, after their latest victory against the German champions lifted them to fourth in the Bundesliga.