The Blues compete with Atletico for a place in the May 24 final in Lisbon against Real Madrid or defending champions Bayern Munich, after falling to a controversial loss to relegation-threatened Sunderland.
It was Mourinho's first Premier League home defeat in 78 matches and the fallout could last for some time, with the Football Association expected to scrutinise incidents involving midfielder Ramires and Chelsea assistant boss Rui Faria.
The FA may also examine Mourinho's post-match comments in which he made a veiled criticism of the match officials and referees' chief Mike Riley, laced with sarcasm.
"If you want to speak about the Premier League you have 19 teams in England that you can speak with," Mourinho said.
"We are lucky to be involved in the Champions League, so we are lucky that in the next two days we don't think about the Premier League and what's happened and what is going to happen because now we only think about (the match)."
Ramires' domestic season could be at a premature end after he caught Sebastian Larsson with a failing arm, while Faria was sent to the stands for angrily approaching fourth official Phil Dowd.
Mourinho, meanwhile, barely hid his contempt after Fabio Borini - on loan from Liverpool - netted the decisive penalty in comments which could lead to him facing further censure from the FA.
Mourinho was returning to the Spanish capital for the first time since his three-year spell at Real Madrid ended, but was in no mood to be charming and declined to speak in Spanish. That was left to David Luiz.
Mourinho declined to discuss in detail his thoughts on Atletico and the curious situation which sees Chelsea likely to face their own goalkeeper, with Thibaut Courtois on loan in Madrid for a third successive season.
It was reported that Chelsea would demand the Spanish side pay a fee of around 3million euros for each game in accordance with their confidential loan agreement, but UEFA announced it expected Courtois to be free to face the Blues.
Mourinho said: "I don't speak about players from other teams."
Mourinho is twice a Champions League winner - with Porto in 2004 and Inter Milan in 2010 - but not with 2012 winners Chelsea. Not yet.
Twice he reached the semi-final as Blues boss, each time losing to Sunday's Premier League opponents Liverpool.
Striker Samuel Eto'o (knee) did not travel, but playmaker Eden Hazard (calf) and goalkeeper Petr Cech (illness) did.
The absence of Eto'o could see Fernando Torres called upon, although Mourinho opted to use Andre Schurrle as a 'false nine' in the previous round at Paris St Germain.
Right-back Branislav Ivanovic is suspended, so Ashley Cole could return at left-back, with Cesar Azpilicueta switching flanks.
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