Andre Schurrle netted twice for the profligate visitors, though the Potters claimed all three points thanks to Oussama Assaidi's stunning 90th-minute strike.
The defeat keeps Chelsea four points adrift of Premier League leaders Arsenal, a gap which could be extended when the Gunners face Everton on Sunday, and the Portuguese blasted his side's failure to convert their pressure into a win.
|4/1||Chelsea are 4/1 with BetVictor to win the Premier League|
“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 after that 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 their performance in the closing stages was below par.
“I think the mentality is changing. The team wants to attack, the team wants to have the ball and the initiative,” he added.
“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 performance 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 give 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.”