Cech suffered a dislocated shoulder in Chelsea's scoreless draw with Atletico Madrid, while Terry picked up an ankle injury.
Cech collided with Raul Garcia in the first half of Chelsea's scoreless draw with Atletico Madrid on Tuesday and was taken to the 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 miss Sunday's Premier League title clash with Liverpool at Anfield along with Chelsea's Champions League semifinal second leg with Atletico at Stamford Bridge on April 30.
John Obi Mikel and Frank Lampard will also be suspended for the second leg but Branislav Ivanovic will be available after serving his ban.