Ronaldo, who sustained a muscle injury in the 1-1 draw at Real Valladolid earlier this month, was withdrawn from the side prior to Saturday's 3-1 win over Espanyol, while Benzema limped off in the 67th minute after setting up Gareth Bale for the opening goal.
Benzema's replacement Alvaro Morata made sure of the points with a double, which was sandwiched by a consolation from Espanyol substitute Pizzi.
Focus will now switch to next Saturday's Champions League showpiece with city rivals Atletico Madrid, and Ancelotti insisted that both Ronaldo and Benzema will be available to play in Lisbon.
"Cristiano was not comfortable. In training yesterday he had confidence," Ancelotti said.
"Benzema as well. When he passed the ball to Bale he had a little discomfort in his hamstring, but neither will have trouble to play in the final.
"It (playing Ronaldo) wasn't a risk, yesterday he had a lot of confidence. He was very happy and wanted to play.
"But in the warm-up he was not comfortable and we decided to remove him from the game to avoid risk.
"When you have a final we are not going to take risks. If today was the final of course we would have risked Cristiano and gambled, but we did not need to take risks today."
Ancelotti also confirmed that Pepe, who has missed the last two games due to a calf injury, is to return to training on Sunday.
"Pepe has improved," the Italian added. "Tomorrow he starts work on the pitch. We are confident he can play.
"Minus (Xabi) Alonso and Jese (Rodriguez), the others will be ready."
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