The Portugal star was anonymous for large periods of the first half and was withdrawn at half-time after complaining of pain in his left hamstring.
Ancelotti said: "Cristiano felt some pain in his left hamstring and was not comfortable. We will do the tests tomorrow. At first it does not seem so serious.”
In the second period James Rodriguez looked to have given Madrid the win with a scrappy late goal, but Raul Garcia levelled with two minutes remaining of normal time to set up an intriguing second leg.
Ancelotti was quick to praise the efforts of James after the game and felt his players had controlled the match throughout.
"James Rodriguez did really well and the whole team was more direct in the second half. His goal will give him confidence," he added.
“I think the team played well, with an extraordinary rhythm, and controlled the play for the whole game. We pressed high up and the three midfielders did well.
“Atletico have a slight advantage but we’ll give it our best to win the title on Friday.”
Angel Di Maria appeared as a late substitute and Ancelotti again faced questions over his future after Atletico boss Diego Simeone said the Argentine was Madrid's best player.
“Di Maria is one of many good players," he replied. "But I think he forgot Cristiano, who won the Ballon d’Or and [Gareth] Bale, who scored in Lisbon.
"Di Maria is a Real Madrid player and I'll use him as I want."
The Italian also revealed he has made a decision over which of his goalkeepers will start the season as first choice, with Iker Casillas coming under the microscope again for Atletico's equalising goal.
"Iker did not have a chance to do anything in that situation as he had a player in front of him. The mistake was at the near post.
“I have decided who will be my first-choice goalkeeper this season, but I’m not going to say who it is.”