Andre Schurrle netted twice for Chelsea, but the Potters claimed all three points thanks to Oussama Assaidi's stunning 90th-minute strike.
The defeat means Chelsea remains well adrift of Premier League leader Arsenal, which faces Everton on Sunday, and Mourinho blasted his side's failure to convert its 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 capitalize 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.”
Despite this latest setback, Mourinho is impressed with the mentality of his team, although he accepted that its performance in the closing stages was below par.
“The team wants to attack, the team wants to have the ball and the initiative,” the former Real Madrid boss argued. “In the last part of the game we didn't play well, because we started playing in a way they (Stoke) can control.”
Mark Hughes, meanwhile, was thrilled with his side's display and hopes the Potters can build on the result as they bid to pull away from the relegation zone.
“I thought it was a fantastic game. I felt from start to finish we put in a real performance,” said the Welsh boss. “We had to recover very quickly from going behind and thought we showed real character and stuck at it after Chelsea gave us a bit of a run around in the first half.
“We’ve set our own standards today and we need to maintain it and if we can we’ll be a very tough side to overcome.”