Andre Schurrle netted twice for the profligate visitors, but the Potters claimed all three points thanks to Oussama Assaidi’s 90th-minute strike.
The defeat means Chelsea remain four points adrift of Premier League leaders Arsenal, who were yet to face Everton yesterday at the time of going to press, and Mourinho blasted his side’s failure to convert their pressure into a win.
“I don’t feel comfortable enough to tell you what I think about the game,” the Portuguese fumed. “We’re in trouble. After 30 minutes we should have been winning 3-0 or 4-0 but we weren’t.
When you play so well and it is so easy you find spaces, and when the three players behind the strikers were playing so well, you have to kill the game, and we didn't.
“We played amazingly well at the beginning of the game, (Juan) Mata, (Eden) Hazard and Schurrle played very, very, well.
“But we didn’t score enough goals and, on top of that you make defensive mistakes and you concede. I think this team is a team that has to score goals; has to capitalise on the production and the way we are playing, because we are not a physical team.
“We are not a team with the conditions to defend against physical teams, so I think we have to score when we have the game in our hands.”
Mourinho also admitted that his team’s performance in the closing stages was below par. “In the last part of the game we didn't play well, because we started playing in a way they (Stoke) can control,” he said.