Atletico coach Diego Simeone faces a hearing after he ran on to the pitch and was sent off by the referee near the end of extra time, the European governing body said in a statement.
Real midfielder Xabi Alonso, who could not play in the match because of suspension, has been charged with breaching general principles of conduct, UEFA added.
Simeone said he had been angry because Real's France defender Raphael Varane flicked the ball at him but the Argentine conceded he should not have acted as he did.
"At that point it was pointless for the player to create that situation," said Simeone.
Alonso's charge is understood to relate to his conduct at the edge of the pitch.
Both teams also face charges of "improper conduct of the team" after receiving five or more yellow cards each during Real's 4-1 win, while fans set off fireworks at the Stadium of Light.
UEFA said the disciplinary panel would hear the case on July 17.
(Reporting by Brian Homewood; editing by Neville Dalton)
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