The world's most expensive player had been due to make his Bernabeu bow in last weekend's clash with Getafe but felt a tweak in his left thigh during the warm-up and was left out by Ancelotti.
Bale underwent tests at the Sanitas hospital in La Moraleja where, according to a medical statement from the club, it was confirmed the Wales international was suffering from muscle fatigue.
Madrid are due to host in-form Atletico on Saturday, with their visitors holding a 100 per cent record after five games and sitting two points ahead of their rivals.
Given Atletico's form, Ancelotti will be hoping to put out his strongest side, which would include Bale.
The Welshman will not be in the squad to take on Elche on Wednesday evening to make sure he is ready for Real's biggest game of the season to date.
The Italian told reporters at Real's press conference: "Gareth Bale trained individually today. He should be fit for Saturday's match.
"He won't be included tomorrow because we have to prepare him well for Saturday. He wasn't happy after the game on Sunday, but his mood has changed quickly because he has begun to think about Saturday's match."
Ancelotti also played down suggestions that Bale had been forced into competitive action too soon after joining Madrid having hardly featured in pre-season for Tottenham.
"I don't think there has been a rush," said Ancelotti.
"He played for just 60 minutes against Villarreal and 30 against Galatasaray. He didn't have any issues heading into the Getafe game, but then the problem arrived.
"It is not a serious muscle injury because if it was he wouldn't have been able to train today or play on Saturday. I don't know what happened, but we won't risk him by putting him on the pitch tomorrow."
Don't forget, you can catch the Madrid derby live on Sky Sports 2 this Saturday from 9.00pm