The left back, on loan from Hamburg, tore his cruciate and medial ligaments in training this week and is unlikely to feature again in 2013-14.
The club confirmed that the Germany international, who is on loan from Hamburg, suffered the blow in the buildup to Saturday's Bundesliga clash with Stuttgart.
Aogo's absence creates another problem for Schalke boss Jens Keller, whose side faces Basel in its final Champions League Group E match on Dec. 11, needing a victory at the Veltins Arena to progress to the last 16.
The left back is the latest in a string of players for the Gelsenkirchen club to suffer ligament issues - Klaas-Jan Huntelaar and Marco Hoger are currently out of action with medial and cruciate damage respectively.
Aogo was loaned out to Schalke in the summer having been at Hamburg, where he has a contract until 2015, since 2008 and he has picked up 12 caps for Germany since his debut in 2010, though his chances of making the World Cup next summer have now plummeted.