The relegation-threatened Black Cats ended Mourinho's 77-match unbeaten home league run with a 2-1 win on April 19.
Mourinho could not hide his anger afterwards behind a sarcastic appraisal of the officials. He has requested a non-personal hearing in the case, the FA has announced.
His assistant Rui Faria, who was dismissed for angrily confronting the match officials, has admitted two charges of misconduct and requested a non-personal hearing.
Midfielder Ramires received a retrospective four-match ban, ending his domestic season, for striking Sebastian Larsson during the loss.
Mourinho and Faria had until 1800BST on Monday to respond to the charges, which were levelled last Wednesday.
A FA statement read: "Jose Mourinho has denied an FA charge and requested a non-personal hearing in relation to comments he made following Chelsea's game against Sunderland on April 19, 2014.
"It is alleged that Mourinho's post-match comments constitute improper conduct, in that they call into question the integrity of the referee appointed to the above fixture (Mike Dean) and/or the integrity of Mr Mike Riley, general manager of the Professional Game Match Officials Limited, and/or the comments bring the game into disrepute.
"In relation to the same fixture, Chelsea assistant manager Rui Faria has admitted two misconduct breaches and requested a non-personal hearing.
"The first breach was that Faria used abusive and/or insulting words towards the fourth official (Phil Dowd). The second breach was that Faria's behaviour following the match referee's request that he leave the technical area amounted to improper conduct.
"A date for both hearings will be set in due course."
It is Mourinho's latest brush with authority this season.
Mourinho challenged a charge related to his dismissal at Aston Villa last month as a point of principle and is considering his options after being hit with an £8,000 penalty, his second of the season after his sending-off against Cardiff.
The Portuguese was tight-lipped on Friday following the charge.
"Every time I speak there is a consequence," Mourinho said.
"Even if I say that a referee was amazing that was a reason to be with a charge.
"I can't say the truth. I don't feel free at all. If you want a better press conference, speak with the FA."
Asked about the British sense of humour and sarcasm, Mourinho said: "So Mr Bean is in jail...
"I told the referee he was amazing, and I repeat: the referee was amazing.
"I was not surprised (by the disciplinary action). In football I'm never surprised."
He was also sarcastic in commenting on Ramires' ban - "He's a lucky guy. We accept the charge because we are happy with it," Mourinho said - and is again unhappy he could be forced to pay a fine.
"When I have to give money, I prefer to do it privately," he said.
"My wife says that charity is anonymous. I prefer to do that than give money because people decide to take money out of my pocket."
- Sports & Recreation
- Rui Faria