The Chelsea goalkeeper collided with Raul Garcia in the first half of the Champions League semi-final first leg against Atletico Madrid, being withdrawn after just 15 minutes
The 31-year-old collided with Raul Garcia after 15 minutes and required lengthy treatment on the pitch before being replaced by Mark Schwarzer and Jose Mourinho confirmed the extent of the injury after the game.
"Petr Cech's season is over," the Chelsea manager told reporters.
Cech had returned to Chelsea's starting side after missing Saturday's 2-1 defeat at home to Sunderland because of a virus, and is joined by captain John Terry, who injured his ankle, on the sidelines.
On-loan Chelsea goalkeeper Thibaut Courtois also started the first leg at the Vicente Calderon.
Reports had initially suggested that the 21-year-old was unable to feature against his parent club unless Atletico paid a fee but Uefa confirmed prior to the semi-final draw that the Belgian was able to play as any contract clause between the two sides was "null, void and unenforceable".