Towards the end of the 3-1 victory over Barcelona at Camp Nou, Ronaldo was handed a second yellow card before reacting by pushing the official in the back.
The forward's actions have led to a five-match ban, and Zidane has acknowledged that he is unhappy with the length of time which the Portuguese superstar will spend on the sidelines.
Zidane told reporters: "I am annoyed, we are annoyed. I do not want to interfere with referees, but when you look at happened and to think that Cristiano will not play for five games, there is something wrong. Five games it is a lot."
As well as Wednesday's second leg at the Bernabeu, Ronaldo will miss Real's first four matches in La Liga.