The Portugal forward, fresh from almost single-handedly getting his country to the World Cup finals with a brilliant hat-trick in the midweek play-off second leg against Sweden, opened the scoring with less than three minutes on the clock at the Estadio de los Juegos Mediterraneos before signalling to the bench early in the second half that he could not continue.
However, with attention now turning to Wednesday's Champions League clash with Galatasaray at the Bernabeu, Ancelotti did not seem overly concerned with the 28-year-old's fitness issue.
"He had a problem with his hamstring. I don't think it's a big problem. It doesn't hurt him," the Italian said on www.realmadrid.com after the match.
"His muscle is a bit tired but I think he'll be better soon.
"Tomorrow he'll have some tests but we think that it's not an important problem. Cristiano started the game with a goal but then he had a little problem."
Ronaldo himself, who now has 35 goals in his last 25 appearances in all competitions, said on Spanish radio network Cadena SER: "It was a blow - it's nothing special."
There remained only one goal in it until after the hour mark, but, despite Ronaldo's absence, the floodgates opened in the final half-hour, with further goals from Karim Benzema, Gareth Bale, Isco and substitute Alvaro Morata sealing the rout.
The victory ended Almeria's three-game winning run in emphatic style, and ensured Real ended the day still six points behind Barcelona after the Primera Division leaders' 4-0 triumph over Granada in the early kick-off.
"I think it was a good game," Ancelotti said. "We didn't concede any goals and that's important.
"The team all played well. We have to carry on this way because we are doing well right now. We've had a lot of problems because of international games and today was a different game and we should be happy."
He was not entirely satisfied, however, adding: "In the last 15 minutes of the first half we lost control of the game a little. We played a bit more slowly, but those are just small details.
"We could have scored a second goal in the first half. We lost a bit of confidence in those 15 minutes, but nothing else."
Ancelotti had to reshuffle his midfield due to an injury to Sami Khedira, and was pleased with how Isco and Asier Illarramendi stepped up.
"Illarra has worked really well over the last two weeks. He's in good shape, the same as Isco, who has worked very well too," the 54-year-old said.
"We've made a few changes to put the players in a more comfortable position. Illarra and Xabi played very well and the team was really balanced especially because of the good work by these two."