Everton manager Roberto Martinez accused Chelsea's players of trying to sway the referee during a bad-tempered 1-0 defeat at Stamford Bridge.
Willian's late winner came after Gareth Barry's red card and a fracas in which Branislav Ivanovic escaped censure for a clash with Everton's James McCarthy.
"It's very clear that what the home team are trying to do is influence the referee," Martinez told BBC Sport.
Mourinho cut short his BBC interview when asked about Chelsea's discipline.
A game that looked destined for stalemate came to life in the closing stages after Barry was shown a second yellow card for a trip on Willian.
As opposing players clashed, Ivanovic locked his arm around McCarthy's neck and appeared to push his head towards the Everton midfielder.
Martinez criticised referee Jonathan Moss for his handling of both incidents.
"To give Barry a second yellow just because of the reaction of the Chelsea players, that is disappointing," he said.
"You don't want to believe that that decision is given because of the reaction of the players. It's something that we constantly see here. We have to allow the authorities to look into it.
"Ivanovic's behaviour is wrong. He grabs McCarthy around his neck in a very forceful manner, then puts his head against him. James McCarthy doesn't react a single bit.
"If you want to be on top of the law, that's a red card and we got nothing out of that moment."
Mourinho has only recently returned from a self-imposed 10-day media silence after accusing the press of influencing the Football Association's decision to punish Chelsea striker Diego Costa for a stamp of Liverpool's Emre Can.
When pressed on the latest flashpoint in a post-match interview with BBC Sport's Jonathan Pearce, Mourinho decided to walk out, telling Pearce: "Sorry, see you tomorrow."
He later conducted a short interview with Pearce in which the subject was avoided, but reacted angrily once again when the Ivanovic incident was raised during a news conference with other media.
"I'm concerned with my reaction because one more question and I leave," he threatened. "And after that you are not happy. The next question for that story, I have to go."
Former Arsenal defender Martin Keown said he does not expect Ivanovic to be punished and suggested Mourinho enjoys the controversy.
"Ivanovic puts his arm around his throat and then the head goes towards him," Keown said on BBC Match of the Day.
"I think he is just about going to get away from this. I don't think there is quite enough of his head making any real contact.
"What it is with Mourinho is that he wants that injustice. For me, it is propaganda. If Ivanovic gets suspended, it just goes towards the cause."