Ronaldo's hamstring problem, which kept him out of Wednesday's 4-1 UEFA Champions League win over Galatasaray, will also see him miss this weekend's home fixture.
The Portuguese forward has been in outstanding form this season, scoring 25 goals in 18 appearances in all competitions for Real Madrid.
"Cristiano won't be available for tomorrow's game because he doesn't feel comfortable yet," Ancelotti said on Friday.
"Cristiano is fully recovered but he is not comfortable and we decided not to risk him. (Angel) Di Maria will play in Cristiano's position tomorrow."
Ancelotti also rubbished suggestions that he had fallen out with experienced defender Sergio Ramos.
The 27-year-old was sent off in the win over Galatasaray, the 17th time he has been dismissed as a Real Madrid player.
Media reports suggested the relationship between the two had broken down and the defender has already been linked with switches to Chelsea and Manchester City.
"The whole world knows how important Ramos is for Real Madrid. There isn't a single problem," he added.
"Sergio Ramos is a very important player for us. He will play and do well tomorrow. Ramos is one of the best central defenders in the world. He has experience and quality.
"I wouldn't sell Ramos for 65 million euros. He is one of the best central defenders in the world."
Ancelotti also said that he did not expect left-back Fabio Coentrao, who is battling a rib injury, to be available until next year.
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