Real Madrid had protested against diving and play-acting by Barcelona players who in turn complained about comments made by their opponents' coach Jose Mourinho.
UEFA themselves have brought charges against both teams who will face a disciplinary hearing on Friday.
"The protests lodged by Real Madrid against the behaviour of the FC Barcelona players during the match and against the red card shown to Pepe are rejected," UEFA said in a statement on Monday.
"In the case of the behaviour of the Barcelona players, it was deemed that there was no common strategy to provoke the Real Madrid player, while in the case of Pepe, the referee's factual decision is upheld.
"As a result, the player Pepe is suspended for the Barcelona-Real Madrid match on May 3.
"The complaint lodged Barcelona against the comments made by the Real Madrid coach Jose Mourinho to the press, was also rejected," UEFA said.
"In this instance, Barcelona have been referred to the proceedings already brought against Jose Mourinho which will be heard... on May 6.
"No new disciplinary proceedings are therefore to be opened against Jose Mourinho on the basis of the complaint lodged by FC Barcelona."
A scuffle on the touchline at half-time led to a red card for Barcelona's reserve goalkeeper Jose Manuel Pinto.
European football's governing body will also investigate the comments by Mourinho, who implied that Barcelona received preferential treatment.
