Uefa rejected fresh protests by both clubs, and said no new charges would be levelled following a bad-tempered semi-final first-leg match last Wednesday, which Barcelona won 2-0.
Instead, Uefa's disciplinary committee will meet on Friday to examine six charges against the two clubs — five for Real, one for Barcelona — including two for the Real coach Jose Mourinho.
Mourinho made offensive comments to match officials and said Uefa actively helped Barcelona reach Champions League finals.
Real reacted by asking Uefa to sanction Daniel Alves, Pedro Rodriguez and Sergio Busquets for feigning injuries.
They also wanted Uefa to look again at a red card shown to Pepe for his tackle on Alves when the match was goalless after an hour.
"In the case of the behaviour of the Barcelona players, it was deemed that there was no common strategy to provoke the Real Madrid players, while in the case of Pepe, the referee's factual decision is upheld," Uefa said in a statement.
"As a result, the player Pepe is suspended for the Barcelona-Real Madrid match [being payed tomorrow]."
Mourinho also will serve a touchline ban at Camp Nou after being sent from the dugout last Wednesday.
Barcelona's additional complaint regarding Mourinho's post-match rant also was rejected by a single member of Uefa's disciplinary committee.
"Barcelona have been referred to the proceedings already brought against Jose Mourinho," the statement said.
On Friday, Uefa will consider charges against Mourinho plus Pepe for his sending off, and Real for their fans throwing missiles and invading the pitch.
Barcelona faces a single charge, for their unused substitute goalkeeper Jose Pinto receiving a red card for his part in a touchline fracas at half-time.