Ronaldo was starting his first home match in over two months following an ankle injury and was at the heart of most of the action in a 4-2 win for Madrid.
Ronaldo set up Madrid's first goal, scored their last, won and then missed a penalty, before seeing red at the death.
The former Manchester United star's first caution came after he removed his shirt while celebrating his goal, while the referee brandished a second yellow when he kicked out at Juanma Ortiz.
The Portugal international will now miss next weekend's game at fourth-placed Valencia, but Pellegrini has refused to come down too hard on the 24-year-old.
"It's a shame that he saw a yellow card for taking his shirt off; he should've avoided that," the Chilean coach told realmadrid.com.
"His double booking was fair because he took his shirt off and because he was involved in a series of fouls.
"He is nevertheless a creative player who doesn't deserve to be sent off; other players make many more fouls and never see a red card."
Pellegrini also played down Ronaldo's lack of celebration following Karim Benzema's goal in the 83rd minute, a strike that saw Madrid establish a 3-2 lead.
"He lamented not scoring from the penalty, which is normal. He always celebrates every goal with his team-mates.
"Each person interprets things as they want, but I can guarantee you he is a good team-mate."