The Portugal winger was unhappy with the display of Mallenco as Barcelona blew the Primera Liga title race wide open by closing the gap on Real and leaders Atletico Madrid to one point.
Real and Ronaldo were angered by the award of two Barcelona penalties, the first of which saw Sergio Ramos sent off before both were converted by hat-trick hero Lionel Messi.
The former Manchester United star also claimed there was a bias towards rivals Barcelona and that some people do not want Real to win the title.
"We are sad because we knew we deserved more, but the fight goes on," Ronaldo told the club's official website.
"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.
"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."