With Mourinho missing from the dugout due to his one-match stadium ban, his side were condemned to the seventh league reverse of their miserable season by Marko Arnautovic's 53rd-minute strike.
They came close to levelling when Pedro hit the post and for long spells saw more of the ball than their opponents.
Ultimately, though, they could not make the most of their chances as the fresh optimism brought about by Wednesday's Champions League win against Dynamo Kiev abruptly fizzled out with another loss to add to the Capital One Cup exit they suffered at the Britannia Stadium last week
Chelsea are now 16th in the Premier League, just three points above the relegation zone.
And despite his name being frequently chanted by Blues fans at the game, the questions about the prospect of Mourinho being sacked will only intensify after this latest poor result.
Speculation abounded as to the Portuguese's possible whereabouts on Saturday, with plenty of references made to the unconfirmed reports of him hiding in a laundry basket during a previous stadium ban - but there was no sign of him at the ground.
Wherever he was it seemed difficult to believe, despite some of his pre-match suggestions, that he was doing anything other than watching the televised match.
And, assuming he was observing from afar, what he saw was a contest that was lively - and feisty - from the off
Xherdan Shaqiri sent an acrobatic effort off-target in the opening seconds before Eden Hazard blazed into the stand at the other end.
Diego Costa engaged in the first of a series of scuffles with Ryan Shawcross, and Erik Pieters was then left bloodied by a more serious, albeit accidental, collision as Pedro's boot connected with the Stoke defender's face.
The visitors broke away soon after with a move that finished disappointingly as Ramires poked wide, and Chelsea's ex-Stoke goalkeeper Asmir Begovic got down to push away a shot by the Potters' former Blues man Glen Johnson.
Chelsea started to dominate possession but could not convert it into a breakthrough, with Jack Butland doing well to palm a looping Ramires shot over and then pulling off a fine save with his foot to keep out a Costa strike, either side of the striker just failing to meet an Hazard delivery across the face of goal.
Jonathan Walters - on the day he signed a new contract with Stoke through to 2018 - did head onto the roof of the Chelsea net, but the hosts may have felt a little relieved to be heading in level at half-time.
They emerged after the break looking full of purpose and within eight minutes had snatched the lead.
Shaqiri fed Johnson, his ball was helped on by Walters and it fell to Arnautovic, who volleyed in.
That only served to increase the fiery atmosphere and Shawcross was swiftly booked for fouling Costa, before Arnautovic and Willian got caught up in a skirmish.
As Stoke looked to keep a grip on things they breathed a sigh of relief as Pedro's curler struck the woodwork and Hazard fired across goal and wide.
It then seemed to sum things up for Chelsea when their substitute Loic Remy hurdled the out-rushing Butland and stumbled as he tried to shoot, missing the target with no penalty being given.
TWEET OF THE MATCH
Stoke goal should've been disallowed because Arnautovic hasn't won as many trophies as John Terry
- talkSPORTDrive (@talkSPORTDrive) jokingly refer to John Terry's comments on Robbie Savage earlier this week as Marko Arnautovic scored the winner for Stoke.
Jack Butland: 7 (out of 10)
Glen Johnson: 8
Ryan Shawcross: 7
Philipp Wollscheid: 7
Erik Pieters: 7
Glenn Whelan: 7
Charlie Adam: 7
Xherdan Shaqiri: 8
Bojan Krkic: 8
Marko Arnautovic: 8
Jonathan Walters: 7
Geoff Cameron: 6
Ibrahim Affelay: 5
Mame Biram Diouf: 5
Asmir Begovic: 6
Cesar Azpilicueta: 6
Kurt Zouma: 6
John Terry: 7
Baba Rahman: 3
Nemanja Matic: 6
Eden Hazard: 8
Diego Costa: 6
Cesc Fabregas: 6
Loic Remy: 6
The Swiss winger looked in fine form for the Potters and certainly gave Chelsea left-back Baba Rahman a torrid evening
Shaqiri beat his man time after time to put Stoke on the offensive and the Ghanaian may have been relieved to be substituted in the second half
MOMENT OF THE MATCH
Marko Arnautovic's goal was a moment of high quality in a game already of a good technical standard
Shaqiri was involved, releasing Glen Johnson with a well-weighted pass and his ball into the box troubled Chelsea
Jonathan Walters was unable to take advantage but Arnautovic showed great agility to volley in acrobatically.
VIEW FROM THE BENCH
Chelsea produced a fluid enough display, which may lead cynics to suggest they play better without Jose Mourinho in charge
But Mourinho, of course, is still the boss and the result will increase the pressure on him considerably
From wherever he was watching on TV, he will have been ruing his side's luck, as his assistants at the ground will have been
They played well but fortune did not favour them
Yet nothing should be taken away from Stoke
They were well organised and motivated by Mark Hughes and they matched Chelsea in most departments
They took their chance and victory was not undeserved.
MOAN OF THE MATCH
Chelsea have moaned about a number of perceived injustices this season, some of them quite wrongly
But they would have good reason to complain about not being given a penalty at a critical time in the second half when Loic Remy appeared to be fouled by Jack Butland
Remy, to his credit, attempted to stay on his feet
Had he gone down, the referee's verdict may have been different
It is a shame if players are not rewarded for their honesty.
WHO'S UP NEXT?
Chelsea v Norwich City, November 21 (Premier League)
Southampton v Stoke City, November 21 (Premier League)
Source : PA