The Argentine stormed onto the pitch on Saturday to confront Real defender Raphael Varane after Cristiano Ronaldo's penalty had sealed a 4-1 extra-time success for Carlo Ancelotti's men.
Simeone exchanged angry words with the Frenchman, who had kicked a ball in his direction after the goal, with the coach then sent from the dugout by referee Bjorn Kuipers.
A statement released by European football's governing body confirmed that Simeone was to be charged, along with the club for "improper conduct" after receiving seven cautions, and for their fans setting off fireworks at Estadio da Luz.
Real midfielder Xabi Alonso has also been charged, after leaving his position in the stands and sprinting down the touchline to celebrate with his team-mates.
Alonso was suspended for the final, having picked up a needless caution in the second leg of his team's semi-final demolition of Bayern Munich.
Real have also been charged for accruing five bookings, and for the use of fireworks by their fans in the stands.
UEFA revealed that the cases will be dealt with on July 17.
