Mourinho walked onto the pitch to speak to referee Chris Foy after Chelsea midfielder Ramires was shown a red card late in the game.
Another Blues player, Willian, had also been dismissed earlier in the match.
Mourinho has until 18:00 GMT on Monday, 24 March, to respond to the Football Association charge.
The Portuguese, whose lead at the top of the Premier League was trimmed to four points as a result of the loss, was critical of Foy after the game at Villa Park.
Ramires was shown a straight red card for a two-footed tackle on Villa’s Karim El Ahmadi, an incident that sparked a touchline fracas.
Mourinho said he was trying to speak to Foy because Ramires was pushed by Villa striker Gabriel Agbonlahor, who had been substituted.
“I don’t know why I was sent off,” Mourinho told BBC Radio 5 live. “I asked, but the referee refused to speak to me.”
Mourinho also said he tried to speak to Foy after the game, but that the referee had refused.