UEFA are probing comments by Real coach Jose Mourinho after last week's first leg when he suggested there was a conspiracy at European football's governing body to help Barca.
The Catalan club won the match at the Bernabeu 2-0 and a 1-1 draw at a rain-lashed Nou Camp on Tuesday was enough to send them through to the final on May 28 in London where they will play Manchester United or Schalke 04.
"We knew we could beat Barca, but the referee didn't let us," Ronaldo, who became the world's most expensive player when he joined Real from United at the end of the 2008/09 season, told reporters.
"Once again it was the referee that didn't allow us to dictate the outcome," he added.
"The referee in the first match (Wolfgang Stark) took away our chances of playing the final. Whoever knows anything about football knows that Barcelona get preferential treatment."
Real were furious that striker Gonzalo Higuain had what they felt was a legitimate goal disallowed by referee Frank de Bleeckere shortly after half-time with the score tied at 0-0.
De Bleeckere ruled that Ronaldo had fouled Barca's former Liverpool midfielder Javier Mascherano, who was playing in central defence on Tuesday, shortly before Higuain curled the ball past Victor Valdes into the net.
"Higuain's goal was good," said Ronaldo, who scored the winner in a 1-0 victory over Barca in the King's Cup (Copa del Rey) Final last month.
"(Gerard) Pique pushed me and I landed on Mascherano. He didn't used to fall to the ground in England, but he's picked up the bad habit of doing it here like everyone else."
OFF-PITCH POWER
Ronaldo pointed to the domestic cup win, the second of four "Clasicos" between the clubs in three competitions in 18 days, as evidence that Real were capable of beating Barca when the officials were neutral.
"Barcelona have a lot of power off the pitch," he said.
"There are no differences between the teams as was seen throughout the four matches.
"We won the Copa del Rey by playing fairly. I don't feel that Barcelona were better than us, but rather that they have a lot of help from the referees."
Barca have an eight-point lead over Real at the top of La Liga with four games left and are closing in on a third consecutive Spanish league title.
