France forward Benzema took a knock to the thigh in a collision with team mate Cristiano Ronaldo in Saturday's 1-0 La Liga win at Malaga and had to be replaced by Angel Di Maria in the 32nd minute.
"He is recovering," Ancelotti told a news conference ahead of Tuesday's last 16, second leg, when Real will start with a 6-1 advantage from the first leg in Gelsenkirchen.
"He cannot play tomorrow along with (Alvaro) Arbeloa and (Sami) Khedira," added the Italian in reference to Real's two other injured players. "We are confident he (Benzema) will be able to recover for Sunday."
Ancelotti said he would be resting some of his regulars at the Bernabeu on Tuesday and Alvaro Morata and Jese would start up front alongside competition top scorer Cristiano Ronaldo.
Ronaldo, Benzema and Gareth Bale each scored twice in the first leg victory in Germany and Real are virtually assured of their place in the draw for the last eight of Europe's elite club competition, which takes place on Friday.
"We will make a few changes but only because we had a tough match (at Malaga) on Saturday night which required a lot of physical effort," Ancelotti said.
"So to allow everyone to recover well we will make some changes with the players who are tired tomorrow."
Ancelotti's side are still alive in all three competitions they are contesting and have a three-point lead over Atletico Madrid at the top of the La Liga ahead of third-placed Barca's visit to the Bernabeu.
A win for Real would put them seven points clear of their arch rivals with nine games left and deal a huge blow to Barca's chances of a fifth domestic league title in six years.
The King's Cup final in Valencia on April 16 is also between Spain's big two, a repeat of the 2011 showpiece which Real won 1-0.
- Sports & Recreation
- Cristiano Ronaldo
- La Liga
- Angel Di Maria
- Alvaro Morata