"Jakub has to expect the worst," the Champions League runners-up said in a statement.
"The Poland international is likely to have torn the anterior cruciate ligament. A more precise diagnosis will have to wait until Sunday."
Blaszczykowski, a force on the right flank, went down following a challenge in the second minute and was later carried off on a stretcher.
Dortmund, who meet Zenit St Petersburg in the Champions League last 16 next month, are already without injured central defenders Mats Hummels and Neven Subotic, who also tore knee ligaments, and playmaker Ilkay Guendogan.
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Third-placed Dortmund have now gone four home league games without a win.
(Reporting by Karolos Grohmann; editing by Tony Jimenez)
