After Atletico defender Jose Maria Gimenez scored the first goal late in a 2-0 win on Wednesday, Simeone turned to his team’s fans and made the gesture.
Simeone said the gesture showed he had courage to make tough selection decisions. Two days later, he apologized.
UEFA says its disciplinary panel will judge the case at a later date. Simeone could be banned from a future game.
The second leg in Italy will be played on March 12.
Juventus coach Massimiliano Allegri also faces an improper conduct charge for his team being late on the field for kickoff.