Eden Hazard dropped to the substitutes bench alongside captain John Terry and Nemanja Matic as Mourinho proved there were no untouchables in his squad.
His hardline approach also followed his outspoken criticism of his players' attitude, but Mourinho's words did not have the desired effect as Chelsea looked vulnerable throughout.
Yacine Brahimi waltzed inside Branislav Ivanovic and behind Pedro, then fired in a shot which Asmir Begovic punched only as far as Andre, who hooked the ball in.
Willian replied with a delightful curling free-kick on the stroke of half-time, but then woeful defending allowed Maicon to head in a corner seven minutes into the second half.
Diego Costa hit the bar, but Porto placed Chelsea under siege and the visitors were grateful to goalkeeper Asmir Begovic for some crucial interventions and a Danilo header came off the post.
Mourinho, who won the 2004 Champions League with Porto, was scathing in his criticism following Saturday's 2-2 draw at Newcastle, which left the defending champions 14th in the Premier League with two wins from seven games.
He appears no closer to finding the answers to Chelsea's poor form.
Costa returned up front after serving two games of a three-match domestic ban, but Hazard, Matic and Terry were substitutes and Loic Remy, Radamel Falcao and Oscar were not even selected to travel.
Mourinho once made a statement at Real Madrid by dropping Iker Casillas and a rotten relationship ensued.
The Blues boss issued a curt reply in relation to Casillas, now the Porto goalkeeper, on the eve of the match, saying he would greet him - probably in the frosty manner he met Arsene Wenger at Stamford Bridge 10 days ago.
Casillas seemed keen to prove a point on his record 152nd Champions League appearance and saved from Cesc Fabregas and then denied Pedro one on one. Pedro should have scored.
Sloppy Chelsea struggled to find any fluidity as Porto probed down Chelsea's right.
Ivanovic avoided punishment for a clumsy challenge on Vincent Aboubakar and, down Chelsea's left, Maxi Pereira shot across goal.
Brahimi next easily cut inside Ivanovic and evaded the back-tracking Pedro before firing a shot which Begovic could only palm out as far as Andre, who volleyed in.
Chelsea equalised after Ramires earned a soft free-kick. Willian curled in from 20 yards, with Casillas flat-footed.
Porto were ahead again with defending uncharacteristic of a Mourinho team, but becoming increasingly familiar this season.
Ruben Neves floated in a corner and Maicon got in front of Ramires, Gary Cahill and Costa to head in at the near post.
Costa beat Casillas with a fine effort which ricocheted off the bar before Hazard replaced John Obi Mikel and soon fired into the side-netting.
Porto piled on the pressure, with Begovic saving from Giannelli Imbula and then scrambling clear at the feet of Brahimi.
Ivanovic headed wide from a Willian corner, but Porto went closer when Danilo's header hit a post.
Costa wanted a handball in the area against Marcano and Kenedy fired wide late on after Costa made space as Chelsea fell to defeat.
TWEET OF THE MATCH
@richardajkeys - "Rarely seen Chelsea hanging on like this. How much longer can Mourinho ignore JT and restoring some order?"
Richard Keys found himself fretting over the state of Chelsea's backline.
Asmir Begovic: 6 (out of 10)
Branislav Ivanovic: 4
Cesar Azpilicueta: 5
Kurt Zouma: 5
Gary Cahill: 5
John Obi Mikel: 5
Cesc Fabregas: 5
Diego Costa: 6
Eden Hazard: 6
Nemanja Matic: 6
Yacine Brahimi: The Algerian showed why he is admired by troubling Chelsea and, in particular, Ivanovic throughout.
MOMENT OF THE MATCH
Diego Costa struck the bar with a fine effort which would, if it had gone in, drawn Chelsea level and might have galvanised the visitors.
VIEW FROM THE BENCH
No one is untouchable was the message prior to the match, with Jose Mourinho questioning his players' attitude. Few expected last season's dazzling star Hazard to drop to the bench, but he did. He sat alongside Matic and captain Terry, who remained out despite defensive fragility. The bench had limited attacking resources as Loic Remy, Radamel Falcao and Oscar were left at home. Hazard, Matic and Kenedy were thrown into the action, but Chelsea could not find an answer.
MOAN OF THE MATCH
What has happened to Ivanovic? The Serbian was a rampaging right-back last season, solid in defence and a fine auxiliary winger. This season he is nothing of the sort and is Chelsea's Achilles heel. Time and again he was exposed by Brahimi.
WHO'S UP NEXT?
Chelsea v Southampton (Barclays Premier League, Saturday, October 3)
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