The Portuguese, who has scored 14 times in the competition this season, was named on the bench for the European contest in Germany, but Ancelotti has said that the attacker was never going to take part.
Los Blancos came close to throwing away their first-leg advantage following a first-half double from Marco Reus, but held on to book their spot in the semi-finals with an aggregate score of 3-2.
"He wasn't okay. We decided not to take any risks," he told AS.
"We're hoping he recovers well and is ready for the semi-finals.
"It isn't a major problem but it was a risk with such a big game. He'll have time to recover well and play. I think he'll be able to play on Saturday."
Ronaldo, who has a knee problem, is not expected to return for the league clash with Almeria this weekend.