The Football Association has given the Portuguese until 6pm on Thursday to respond to the charge.
There were a number of controversial incidents in the game, none more so than Chelsea's disputed equaliser, and Mourinho was sent to the stands by referee Anthony Taylor after losing his cool.
The nature of the offence means Mourinho is most likely to face a fine, rather than a ban.
Mourinho went to sit with the fans, making the day of those he sat next to, but his own frustration was clear.
Speaking earlier on Monday, prior to the FA's announcement, Mourinho insisted he did not understand his sending off.
"I don't know the reason why the referee stopped me doing my work," he said.
"Until that moment (when he is informed why) I'm not going to make any comment.
"To be with the fans was not funny. It's frustrating.
"You want to communicate with the players and you couldn't do it."
While he would not comment on his own conduct, Mourinho had plenty to say about that of Cardiff.
Eden Hazard scored the controversial equaliser after Samuel Eto'o dispossessed Cardiff's David Marshall as the goalkeeper bounced the ball, contrary to FIFA rules.
That brought lengthy complaints from the Welsh club, but Mourinho had little sympathy.
Speaking on Chelsea's arrival in Germany at Dusseldorf airport, ahead of Tuesday's Champions League Group E clash at Schalke in Gelsenkirchen, Mourinho said: "If I was in that game and I was paying my ticket, I would be worried with the fact that every time the ball was out or stopped and our opponent had to put the ball back in the game, it took a median (average) of 21.5 seconds. That is a waste of money.
"When you multiply that by the number of times the game was stopped, you pay for 90 minutes but you see 55 or 60.
"For me, that's breaking the rules."
Mourinho insisted Eto'o's interception was an "intelligent action" and that Marshall's actions were a warning to aspiring goalkeepers, including his own son.
The Portuguese added: "When I arrived home the first thing I told my kids who like to play goalkeeper: 'See the goal and don't be silly?' And he's 12."
Mourinho disagreed with FIFA's law 12, governing the incident, which states "the goalkeeper is considered to be in possession of the ball while in the act of bouncing it on the ground or tossing it into the air".
He added: "If, in this moment, FIFA says that it's a foul, it's a foul.
"But I think Samuel did well. Maybe the referee did wrong.
"In my opinion, that should be allowed as it was for years. No contact with the goalkeeper.
"The goalkeeper has six seconds to have the ball. They had almost half a minute. That's breaking the rules."
Mourinho was also asked about another controversial 'goal' this weekend, when Stefan Kiessling had one awarded for Bayer Leverkusen when the ball went through a hole in the net.
Mourinho said: "If I was the manager of Leverkusen, I would ask to repeat the game.
"If I was the manager of Hoffenheim, I would do the same.
"If I was working in the German Bundesliga - and you are one of the European countries that is not in economical problems - I don't understand why you don't spend a few million (euros) to bring technology on the line.
"If it was the Portuguese or the Greek league, I would say no chance. But with the German one, I don't know why you don't do it."
- Sports & Recreation