The Portuguese was playing in only his third La Liga match of the campaign after recovering from an injury he had picked up in the final of the 2016 European Championship.
Zidane had previously stated that he will introduce Ronaldo progressively into playing again, and also substituted the player on his return to the team during a 5-2 win over Osasuna, a game that saw the 31-year-old get on the score sheet.
On the weekend, though, Ronaldo failed to hit the back of the net, although his second-half shot led to a goal when, after it hit the goalkeeper, Karim Benzema tapped in the rebound to give his team a 2-1 lead.
The Portugal captain was taken off in the 72nd minute, and he was visibly upset with the decision to do so. He tried to contain his anger as he walked off the pitch and even shook hands with Zidane, but did not make any eye contact with his coach.
After passing the tactician, Ronaldo was seen mumbling, and did not stop when he reached his seat on the bench, with some reports suggesting he was directing swear words at the coach.