The 22-year-old, who joined Bayern from Barcelona this summer, suffered the ligament damage in Saturday's 2-0 win over Nuremberg.
"He will be out of action for more than two months - possibly until halfway through November," Guardiola told Bild.
"He played on for more than 20 minutes after picking up the injury, which shows that he has a lot of character."
"This is a huge blow and we will really miss him. He has certain abilities that others don't possess. We will have to find other solutions."
Bayern are currently leading Freiburg 1-0 in the Bundesliga.