The 29-year-old is not expected to be a doubt for the Champions League final despite being forced from the field prior to kick-off
The 29-year-old suffered a hamstring problem in the 1-1 draw with Real Valladolid on May 7 but was passed fit to take his place in the side this afternoon.
However, Ronaldo left the field shaking his head in disappointment after feeling discomfort during his pre-match preparations and has been replaced by Isco in the starting line-up.
His participation in the Champions League final against Atletico Madrid had been thrown into doubt with the two sides set to go head-to-head in just seven days time, but Ancelotti insists his withdrawal was purely a precaution.
He said: "Ronaldo was not comfortable before the game after the good work yesterday in the training session, so we cannot take risks. We've done a test and it looks like a small contracture. We're calm because we have time to recover."
The Portugal captain will also be hopeful the problem is not serious enough to endanger his chances of playing in the World Cup this summer.
A goal on Saturday would have taken Ronaldo on to 31 strikes for the season and seen him scoop the Golden Shoe ahead of Luis Suarez, but the pair will now share the prize.