The Spaniard was sent off after a clash with Everton midfielder Gareth Barry in the 84th minute of Chelsea’s 2-0 defeat at Goodison Park.
Costa, 27, appeared to bite Barry in the incident, although both players have denied that happened.
However, the Football Association has now charged Costa for his behaviour after being shown a second yellow card.
“It is alleged his behaviour, after being shown a second yellow card in the game, amounted to improper conduct,” the FA said in a statement.
The player has until 18:00 GMT on Thursday, 17 March to respond to the charge.
He has also been given until Wednesday to provide his observations to the FA over an alleged gesture made towards Everton supporters while leaving the pitch at half-time.