The Argentinian celebrated his side's first goal in their 2-0 Champions League last 16 first win over Juventus on February 20 by grasping his genitals and thrusting out his groin.
Simeone apologised for his behaviour the following day and said it was to recognise the courage his team showed in the victory.
Juve's Massimiliano Allegri and the Italian club also face disciplinary action for the late kick-off of the game in the Spanish capital.
Atletico also face charges that their fans blocked stairways and threw objects during the match.
No date for the hearing has been set by the governing body.
The second leg of the tie will be played in Turin on March 12.