Andre Schurrle opened the scoring for Mourinho's men at the Britannia Stadium, but goals from Peter Crouch and Stephen Ireland either side of half-time put Stoke in front.
Germany forward Schurrle struck again to equalise three minutes after Ireland had put Stoke in front but substitute Oussama Assaidi scored a dramatic late winner to stun Chelsea.
The London club could have been just a point behind Arsenal with a win on Saturday, but if Arsene Wenger's side beat Everton on Sunday they will be seven points clear at the summit.
Mourinho was left to rue Chelsea's charitable defending and wastefulness in front of goal as they suffered a third Premier League defeat of the season.
"I don't feel comfortable enough to tell you what I think about the game. We're in trouble," said the Portuguese.
"It is a concern (conceding so many goals). I don't like it, I don't organise my teams to be like this.
"I could see that result happening because after half an hour we should have been winning three or four nil - and we weren't."
However, Mourinho insisted that it was not all doom and gloom.
He added: "Maybe tomorrow we are seven points from the leader but when you see us in relation to Man City, Man Utd, Tottenham, Liverpool, I think we are not doing bad."
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