Ronaldo, who has a record 16 goals in the latest edition of Europe's elite club competition, has had a series of niggling muscle injuries in recent weeks and has not played since limping out of a La Liga match at Real Valladolid on May 7.
Benzema hurt a thigh muscle in Saturday's 3-1 win at home to Espanyol, while Pepe has been out since damaging a calf in the Valladolid game.
"Cristiano is fine, he has trained well," Ancelotti told a news conference ahead of Real's last training session before the showpiece match at Benfica's Stadium of Light.
"We have to assess the condition of Pepe and Benzema because they have not trained this week," added the Italian, who is seeking to become the second coach after Liverpool's Bob Paisley to win the European Cup three times.
"After tonight's training session we will take the decision on tomorrow's game."
The coach's biggest headache is in midfield, however, where he needs to decide who will replace the suspended Xabi Alonso.
Real's success this season has in large part been down to the control Spain international Alonso gives them with his distribution skills and tackling prowess.
Asier Illarramendi, who has failed to convince in his debut season, or Sami Khedira, who only recently returned after knee surgery, are two options.
"I have one more night to think about it and tomorrow I will make a decision," said Ancelotti, who won the European Cup with AC Milan twice as a player and twice as a coach.
He added that his "dream" was to see a performance from his team similar to the one they produced in the semi-final, second leg at Bayern Munich, when Real thrashed the holders 4-0 at the Allianz Arena to go through 5-0 on aggregate.
"If we play like we did against Bayern we have a chance," said Ancelotti.
"A lot goes through your mind before a game like this. What matters is to be calm, train well, to be on top of things and give the team clear instructions.
"Rather than thinking about pre-game speeches, my main focus is just on the tactics and those instructions to the players, how to play the game."
Saturday's clash between the La Liga rivals and cross-town neighbours is the first final featuring two teams from the same city in the 59-year history of the competition.
Atletico are appearing in their second final after they lost to Bayern Munich in 1974 after a replay and are seeking their debut European crown having wrapped up their first La Liga title since 1996 at the weekend.
They will be trying to deny Real, through to their 13th European Cup showpiece match and their first since their last continental triumph in 2002, a record-extending 10th title.
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