The Brazilian has been criticised by Real fans for below-par performances and hinted last week he wanted to leave. On Thursday Real's new president Fernando Martin said he would not put up with players who failed to put in the required effort.
Real coach Juan Ramon Lopez Caro said the player had been left out for tactical reasons.
"I don't think he is being singled out for what happened during the week," Ronaldo's Brazil and Real team mate Julio Baptista told reporters.
"He wasn't angry with the decision.
"On form he is the best striker in the world. We need to remain calm. Next Wednesday we have an important game and he will be well rested for it."
Raul or Antonio Cassano are expected to start up front. Next week Real travel to London to play Arsenal in their Champions League first knockout round tie, trailing from the first leg 1-0.
Real midfielder Guti has recovered from a thigh injury and returned to the squad for Saturday.
Florentino Perez resigned as Real president on Monday and blamed the poor attitude shown by some of his players for his decision.
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