UEFA said the case would be heard by its appeals body on May 16 in the latest twist following the bad-tempered clash between Spain's biggest two clubs.
Barcelona won the first leg 2-0 at the Bernabeu on April 27 and qualified for the final with a 1-1 draw in the return at the Nou Camp on Tuesday.
The club said Barcelona had shown "non-sporting conduct" and their players had "persistently simulated aggression against them (Real) with the sole aim of provoking errors from the referee," while adding that Pepe's dismissal had been unfair.
The protest was dismissed on Monday when UEFA also threw out Barca's complaint against Real over comments by the Madrid club's coach Jose Mourinho.
Barca's reserve goalkeeper Jose Manuel Pinto, sent off in a touchline skirmish in the same game, will also face disciplinary proceedings.
