The Portuguese international was last night deployed as a second striker, behind Kaka, in contrast to the previous two games against Lyon and Paris St Germain, in which he played in a more central role.
This prompted speculation that Ancelotti was experimenting with a formation in preparation for the signing of Tottenham star Gareth Bale, who normally plays in a similar role to the Portuguese, on the left side of the attack behind the striker.
Ronaldo has in the past explained that he does not enjoy playing as a centre-forward, preferring a freer role, and after the game Ancelotti made it clear that the forward needed to be played where he felt most comfortable.
Quoted in AS, he told reporters: "Cristiano needs to play in the position that he wants to.
"I will not change his position because he is comfortable in his usual position. He is the one who has to chose where he plays on the pitch."
Angel Di Maria gave Madrid a first-half lead which substitute Karim Benzema doubled in the second period.
Jose Villarreal pulled one back for the Galaxy before Benzema headed in the final goal of the game thanks to a cross from Di Maria.
Ancelotti was pleased with the partnership between the Frenchman and the Argentinian.
He said: "They both played well and scored, but the fundamental thing was that we wanted to play in a compact way, and the team did that.
"It was a good game for us. Cristiano Ronaldo and Kaka also played well together and created a number of chances.
"On the whole, we played very well. I'm very satisfied, we tried to play good football, and that's the most important thing for me."
Isco, who provided Benzema's first goal with an exquisite long ball, explained he was fitting well into the team.
"My team-mates have made it easy for me to adapt," he told the club's official website.
"I always try and play the best football and I'm happy with how things are going up to now.
"We are getting to know each other better in time for the start of the league season. There is still work to do, but we have only just begun. We have to keep training so we can hit our peak. I'm happy with our performance and the win and we have to keep going in the same direction."
The victory means that Madrid will face Everton on Saturday in Los Angeles in their next game in the Guinness International Champions Cup.