Ronaldo, Real's top scorer this season, apparently hurt himself in the warm-up before Saturday's 3-1 La Liga victory over Espanyol at the Bernabeu and was replaced at the last minute by Isco.
However, Ancelotti said it was nothing to be concerned about and the Portugal captain, who has been troubled by a thigh injury in recent weeks, had merely been rested as a precaution.
Benzema limped out of the match with just over 20 minutes remaining with what Ancelotti described as a twinge in his adductor muscle.
"Cristiano wasn't comfortable in the warm-up and we decided not to take any risks," said the Italian.
"We are not worried because we think he can play the Champions League final.
"Benzema had a twinge in the adductor and he shouldn't have any problem in playing the final."
Ancelotti added that centre-back Pepe, who has been suffering with a calf problem, is recovering well and the club are confident he will also play against Atletico.
Ronaldo's absence from the Espanyol game meant he was unable to add to his tally of 31 league goals this season and as a result he will share the European Golden Boot with Liverpool's Luis Suarez who netted 31 times for the Reds in the Premier League.
Watch the Champions League final live on Sky Sports 1 next Saturday evening.