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.
Real Madrid had accused Barca players of play-acting and diving during the Bernabeu game.
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.
The controversial Portuguese belittled the achievements of his counterpart Pep Guardiola and suggested there was a conspiracy among referees to favour the Catalan club.
The saga will continue on Friday when Real face a UEFA disciplinary hearing over their own behaviour, including the red card given to Pepe plus allegations of missile-throwing and a pitch invasion.
The tribunal will also look into the red card against Mourinho for his protests over the Pepe sending-off and his subsequent comments about Barcelona.
Barca's reserve goalkeeper Jose Manuel Pinto, sent off in a touchline skirmish in the same game, will also face disciplinary proceedings.
