The Turkey international was initially ruled out for three weeks after it was revealed he suffered tendon damage in training.
However, Sahin is now set for a longer spell on the sidelines after undergoing an operation on his left knee.
A statement on the club's official website said: "Nuri Sahin has had surgery on Wednesday in the Isar Clinic in Platt Park Ling.
"Dr. Heinz-Jurgen Eichhorn removed inflamed tissue from Sahin's left knee during surgery. Borussia Dortmund team doctor Markus Braun based an approximately two-month rehabilitation period for the Turkish national player."
Dortmund coach Jurgen Klopp has had to contend with a lengthy injury list at the start of the season, with Jakub Blaszczykowski and Ilkay Gundogan among his other absentees.