Mourinho was sent to the stands by referee Anthony Taylor midway through the second half when he vented his frustration after Branislav Ivanovic was warned about time-wasting while taking a throw-in.
He now faces the prospect of further punishment, although he is more likely to receive a fine than a touchline ban. He has until 1800 BST on Thursday to respond to the charge.
According to Mourinho’s assistant, Steve Holland, the Blues boss had been “furious” during Saturday’s game as he felt Cardiff had been guilty of “clear time-wasting” throughout the first hour.
Speaking at a news conference prior to the FA announcement on Monday, Mourinho said he was not amused at having to sit among the Blues fans as the home side secured the victory.
“To be with the fans was not funny,” he said. “It's frustrating. You want to communicate with the players and you couldn't do it.”
He added: “I don't know the reason why the referee stopped me doing my work. Until that moment I'm not going to make any comment.”
That was not the only controversy to emerge from the match. Eden Hazard’s equaliser had come after Samuel Eto’o knocked the ball away from Cardiff goalkeeper David Marshall as he bounced the ball. In doing so, Eto’o contravened FIFA’s law 12, but Mourinho felt the striker’s action was “intelligent”.
“If, in this moment, FIFA says that it's a foul, it's a foul, but I think Samuel did well,” he said. “Maybe the referee did wrong -- I don't know, to be fair -- but 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.”
He added: “If I was in that game and I was paying for 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.”
Information from the Press Association was used in this report