The German international sustained the injury in Wednesday night’s 2-0 victory over Watford.
Gundogan will now be assessed further to discover the exact extent of his injury.
Guardiola said: "It's so so difficult for him, it's sad for him, we're going to miss him a lot, it's unlucky, but that's football."
The manager added: “Now we need him to feel we are there and wait and come back safe. He’s going to be operated (upon) and be back as soon as possible.”
Gundogan joined the Club in June 2016 from Borussia Dortmund. The 26-year-old has made 16 appearances for the Blues, scoring five goals, and has become a popular member of the squad.
We wish him a speedy recovery.