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The Uruguay international was substituted during the first half of the defeat after fracturing his tibia and fibula.
Muslera came off his line to make a brilliant save from Milan Skoda, only to suffer the injury as he collided with the Czech forward.
In a statement, Galatasaray said: "Fernando Muslera, who sustained an injury causing bone fractures in his tibia and fibula, is subject to an examination today and will be planned an operation accordingly."
Galatasaray's loss left them in third place, six points adrift of Trabzonspor and Istanbul Basaksehir.
