The 22-year-old Borussia Dortmund midfielder scored Germany's first goal but was then taken off midway through the first half.
Guendogan's participation was in doubt until the last moment and he needed injections before the game.
"According to team doctor Markus Braun the problem with his back has now become worse instead of improving," the club said on their website (www.bvb.de).
Dortmund host promoted Eintracht Braunschweig in the Bundesliga on Sunday.
(Reporting by Karolos Grohmann; editing by Tony Jimenez)
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