Ancelotti said centre back Pepe, who has been suffering with a calf problem, was recovering well and the club were confident he could play against Atletico.
Ronaldo has recovered from a series of niggling injuries and is fit to play in Saturday's La Liga game at home to Espanyol, coach Ancelotti said.
Real are two points behind Barca in third before their game in hand at second-from-bottom Valladolid.
Khedira hasn't played since tearing a ligament in his right knee while playing for his country in a friendly against Italy.
Casillas will play for Real Madrid in the Spanish league for the first time in more than a year to maintain his form for the upcoming Champions League final.
"We have achieved it through hard work and if you do it with quality players it's much easier to win," Ancelotti said.
Bayern Munich coach Pep Guardiola still believes in possession-based football and cannot alter his feelings about the way the game should be played.
The Real coach praised his team for beating holders Bayern Munich in Champions League semi-final first leg on Wednesday.
Bale, who has been suffering from flu, trained with the rest of the squad earlier on Tuesday but could not join up with them later at their hotel.
Ronaldo will miss Wednesday's King's Cup final against Barcelona after failing to recover from knee and thigh muscle problems.
The Portuguese international sat out the weekend La Liga match with Real Sociedad after leaving last week's first leg against Dortmund with an injury.
Ronaldo has been complaining of discomfort in his left knee in recent weeks and has played on while receiving treatment from Real's medical staff.
"It's a slight knee problem and I'm not worried about it," Ancelotti told a news conference.
In a bid to win their 10th European title, Real Madrid will face Borussia Dortmund in their quarter-final first leg tie at Santiago Bernabeu on Wednesday.
Arbeloa will be sidelined for nearly two months by a knee injury, putting the Spain international's participation at the World Cup in jeopardy.
Carlo Ancelotti:The man who can secure the "decima" that has eluded Real since their last Champions League triumph in 2002
Zinedine Zidane's son Enzo has won the chance to be selected for the French Under-19 squad, a potential first step along the path of his father.
Bale's debut season in Spain has been disrupted by a series of minor injuries following his move from Tottenham Hotspur for a record fee.
Real Madrid can pile the pressure on La Liga leaders Barcelona and Atletico Madrid by taking all the three points against Betis.
The 25-year-old insisted it was "a natural gesture" and said he apologised if anyone had found it offensive.
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