The Dutchman partially tore a ligament in the Ruhr valley derby on Saturday after a collision with his own keeper and has been ruled out for some weeks, but will not need surgery.
His absence, however, could prove vital as Schalke look to advance after their last-16, first-leg 1-1 draw in Istanbul.
For club bosses, however, victory over Dortmund in Germany's biggest derby overshadowed the bad news of Huntelaar's injury and was exactly the boost Schalke needed after a bad run.
"That is balm for our soul," said Schalke sports director Horst Heldt after Saturday's 2-1 victory that enabled them to climb back into the Bundesliga top four.
"To deservedly beat the champions does not happen every day and it gives us courage for the tasks ahead," Heldt told reporters.
Schalke have enjoyed a rollercoaster season that has left the club with only the Champions League title to fight for.
They began well and stayed close to leaders Bayern Munich until late in the year when they imploded, exiting the German Cup and dropping down the table.
Their win on Saturday was their third straight success after a miserable run of one victory in their previous 11 matches.
"Galatasaray will be a different game but those at Galatasaray will also have seen our game against Dortmund. I am convinced we will take that next big step," Heldt added.
Schalke, who together with Juventus and Borussia Dortmund are the only undefeated teams left in the competition, last made it to the last eight in 2011 on their way to the semi-final of Europe's premier club competition.
They will be without hard-tackling midfielder Jermaine Jones, who is suspended having received a yellow card in the first leg.
The Turkish side were far less successful in their dress rehearsal, losing 1-0 at home to mid-table Genclerbirligi with January signing Didier Drogba missing a penalty.
That prompted a warning from coach Fatih Terim that a similar performance would be punished more harshly by Schalke.
"Pull yourselves together," the coach was quoted by Turkish media as telling his players after Friday's league defeat. "I do not want to see such a performance against Schalke."
Galatasaray will put their faith in their newly-formed attacking trio of Wesley Sneijder, Drogba and the Champions League's second highest goalscorer, Burak Yilmaz, to help them to advance past Schalke.
The game will also mark the return to Gelsenkirchen of midfielder Hamit Altintop, who spent four seasons with Schalke from 2003.
Galatasaray are still leading the Turkish championship by four points despite Friday's defeat.
Yilmaz, who has scored seven of his team's eight goals in the Champions League this season, is also the leading goalscorer domestically, and Terim needs his side's attacking trio to hit top form.
The second leg could have an unusual atmosphere as Gelsenkirchen is home to a large number of Turks who have been avidly buying tickets.
Turkish media reported the Istanbul club will wear shirts with "Istanbul 2020" logos to support Turkey's bid to host the Olympics, competing with Tokyo and Madrid.
Schalke 04: 34-Timo Hildebrand; 22-Atsuto Uchida, 4-Benedikt Hoewedes, 32-Joel Matip, 35-Sead Kolasinac; 17-Jefferson Farfan, 12-Marco Hoeger, 33-Roman Neutstaedter, 31-Julian Draxler, 9-Michel Bastos; 25-Klaas-Jan Huntelaar.
Galatasaray: 25-Fernando Muslera; 55-Sabri Sarioglu, 26-Semih Kaya, 13-Dany Nounkeu, 11-Albert Riera; 4-Hamit Altintop, 10-Felipe Melo, 8-Selcuk Inan, 14-Wesley Sneijder; 17-Burak Yilmaz, 12-Didier Drogba