The goalkeeper suffered a dislocated shoulder in Chelsea's goalless draw with Atletico Madrid, while the club's captain picked up an ankle injury
Cech collided with Raul Garcia in the first half of Chelsea's goalless draw with Atletico Madrid on Tuesday evening and was taken straight to hospital for scans.
Terry, meanwhile, landed awkwardly on his ankle after Diego Costa stepped on his foot in the 71st minute. The Chelsea captain attempted to continue but was forced to withdraw as he was unable to move freely.
"Petr Cech's season is over," Mourinho told reporters after the match.
"For John [Terry], we will have to play the final for him to play again."
The duo will now miss Sunday's Premier League title clash with Liverpool at Anfield along with Chelsea's Champions League semi-final second leg with Atletico at Stamford Bridge on April 30.
John Obi Mikel and Frank Lampard will also be absent for the second leg due to suspension but Branislav Ivanovic will be available after serving his ban.