Real's regular centre-backs Sergio Ramos and Pepe are injured while left-back Marcelo is also suspended for the game, when victory for leaders Real would give them a 10-point cushion over third-placed Atletico.
Frenchman Raphael Varane has been playing alongside Ramos recently, and has been involved in some important games for the club, but the homegrown Nacho Fernandez has been given little playing time since he made his debut under Jose Mourinho in 2011.
While Nacho is quick he is not tall, and Ancelotti says they lack height against a physical Atletico side that might choose to play Mario Mandzukic in attack rather than Fernando Torres because of the Croat's aerial ability.
"We are limited in this area and it is a problem for us," Ancelotti told a news conference on Friday. "It was the same for us against Sevilla (when Real won 2-1), where they had more powerful players than us and we managed to cope with it.
"We will use others to get back and help out the smaller players.
"The injury to Sergio (Ramos) is serious but I have complete confidence in Varane and Nacho. They are both very good players and are looking forward to the game, especially Nacho, and I am sure that he will be fine."
Real have suffered a series of injuries so far this season. They are also missing Luka Modric and James Rodriguez further up the pitch.
"A lot of the problems have just meant players have been out for a short amount of time, but others like Sergio's are more important," Ancelotti said.
"There have been too many injuries for midfield players though, and this is a worry."
Atletico have been criticised in some games this season for being too aggressive, but Ancelotti denied this was a concern.
"We don't have any fear. They are a team which works well above all defensively and they are one of the best sides in the world," the Italian said.
"We are focussing on the best way to make it difficult for them and to beat them."
Real are four points ahead of second-placed Barcelona, who visit Athletic Bilbao on Sunday.
(Editing by Stephen Wood)
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