The Atletico Madrid boss stormed on to the field in the wake of Real Madrid's fourth goal in Lisbon on Saturday night, angry with France defender Raphael Varane.
The Real player had kicked the ball towards Simeone as he walked back after Cristiano Ronaldo's penalty made it 4-1 and, after whacking it back at him, Simeone stormed on the field and had to be restrained as he went for the player.
He will be dealt with, UEFA confirmed on its website, on July 17.
Real midfielder Xabi Alonso has also been charged with improper conduct.
The Spain international was banned for the match and as such could not be on the bench but, when Gareth Bale scored what proved to be the winning goal, he ran down the touchline to join his team-mates in celebration.
Both sides have also been charged for receiving more than five yellow cards each.
- Sports & Recreation
- Real Madrid
- Cristiano Ronaldo
- Real player
- Xabi Alonso
- Atletico Madrid