The Portugal winger scored Real’s third goal from a penalty he himself won, with Dani Alves’ foul clearly outside the penalty area.
Despite that gift, though, Real and Ronaldo were angered by two subsequent Barcelona penalties, the first of which saw Sergio Ramos sent off before both were converted by hat-trick hero Lionel Messi.
Ronaldo told realmadrid.com: “We are sad because we knew we deserved more, but the fight goes on.
“It is difficult because a lot of people did not want us to win and Barcelona would have been out of it.
“Maybe they don’t want Real Madrid to win this Liga. I’ve been here for five years, so I know how a lot of things are and I hope to win it regardless of this.
“It’s a feeling of sadness after being 3-2 up and controlling the game. The referee made some unbelievable decisions, but you have to carry on.”
Undiano Mallenco refereed at the 2010 World Cup, has extensive Champions League experience and was named Spain’s top referee in 2005 and 2007 – but Ronaldo accused him of being too nervous to take control of Sunday’s big game.
“There were a lot of errors in one match,” he said. “In a Real Madrid-Barcelona (match) you have to have a referee who is up to the game.
“I don’t want to look for excuses but if you look at the 90 minutes the referee made a lot of mistakes. Really bad.
“In my opinion he was not up to a match of this stature. I looked at him and he was pale, that’s because he was so nervous and he was unable to make the right decisions.
“Real Madrid is the biggest club and that creates a lot of envy around it. You can say that the treatment is the same, but it’s not.”
Barca coach Gerardo Martino declared La Liga’s title race back on after his team’s thrilling win.
Barca took a fourth-minute lead through Andres Iniesta but then twice trailed as Karim Benzema struck a first-half brace and – after Messi levelled – Ronaldo’s penalty restored Madrid’s lead early in the second half.
But everything changed when Ramos felled Neymar in the area, and Messi took centre stage.
“La Liga is not over,” Martino said. “We were given up for dead but with this result we are right back in it.
“This was our last chance. We did not want to be left out.”
Barca stay third with the win, but are now only one point from the summit with Atletico Madrid topping Real on head-to-head record.
Messi’s hat-trick took him to 236 goals in the league, overtaking Hugo Sanchez for second in La Liga history.
“It’s difficult to talk about him,” Martino said. “You run out of things to say.
“He is still breaking records. He plays so many great games, especially when it counts.”
Neymar’s performance brought some criticism, but Martino defended the expensive Brazilian.
“He did not have the best game, but the turning point – the red card of Ramos – comes from him,” he said.
“At that moment he was on a phenomenal run. He’s only 21 but he can handle the big games.”
If they could have hung on to either of the leads they held, Madrid would be seven points clear of Barca, but coach Carlo Ancelotti downplayed the damage done to his side’s ambitions.
“It does not matter so much because we are still in contention for the title,” he said.
“We played well. We did not deserve to lose.”