The stalemate came at a cost for Mourinho and the Blues as Cech went off after 18 minutes with a shoulder injury and captain John Terry departed after 72 minutes with a foot problem.
Cech was injured as he punched the ball from underneath his own crossbar, with David Luiz pushing Raul Garcia into the Chelsea goalkeeper who hit the ground with a thud and was replaced by Mark Schwarzer.
The Czech Republic goalkeeper will miss the final three matches of the Premier League season, beginning at leaders Liverpool on Sunday, as well as the conclusion to the European campaign.
Mourinho said: "Petr Cech's season over. Don't ask me technically, but season over.
"And John - we have to play the final for him to play with us."
Chelsea lost 2-1 to Sunderland in the Premier League last Saturday to leave the European Cup they won in 2012 their most likely trophy chance this term.
Given the Blues are five points behind Liverpool ahead of the trip to Anfield, Mourinho believes Europe is now the priority.
But he will consult the Chelsea hierarchy before deciding which players to field at Anfield, with his preference to opt for those who will not feature against Atletico next Wednesday due to the proximity of the matches.
"I can't decide by myself," Mourinho said.
"I think that's a decision I have to listen the club. I'm just a piece, I'm just the manager and no more than that.
"I have to listen to the club. I think the fact that the match is on Sunday I think puts the problem not in my hands.
"We represent English football and we are the only English team that is European competition. Spain has four and gave them all the conditions to try to have success.
"I know what I would do, but I'm not the club. I have to speak with the club.
"I would play with the players that are not going to play Wednesday."
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- John Obi Mikel
- John Terry
- Frank Lampard