Zidane replaced the three-time World Player of the Year with Madrid leading 2-1 18 minutes from time, but an unhappy Ronaldo watched from the bench as Sergio Araujo equalised to ensure Real dropped points for the second time in four days.
"I have to take him off sometimes and tonight we did it," said Zidane. "That isn't going to change what we are going to do continue to do."
At the forefront of Zidane's mind was Real's huge Champions League clash away to Borussia Dortmund on Tuesday.
However, Ronaldo endured a poor night in front of goal as he fluffed a great chance from Alvaro Morata's cut-back before half-time and fired straight at Javi Varas in the build-up to Madrid's second goal.
"We have a game on Tuesday and I thought it was the time to take him off, 20 minutes from the end, thinking about Tuesday," added Zidane. "I know he always wants to play and always wants to stay on the field, but
I also have to think about the players and for me it was best to rest and think about Tuesday."
Ronaldo has completed 90 minutes just twice this season, though, as he was also replaced early on his return from a knee ligament injury against Osasuna earlier this month and missed last weekend's win at Espanyol due to illness.
Real's lead over Barcelona at the top of the table now stands at a solitary point having failed to bounce back from a 1-1 draw with Villarreal on Wednesday that snapped a 16-game winning streak in La Liga.
Of most concern for Madrid is their leaky defence as they have now kept just one clean sheet in their last six games.
"Sometimes there are games like this where you have the chances to win and you don't take them," continued Zidane. "I think there is a lack of concentration in the second goal. I have to analyse it, but I am not going to complain. Playing like this for 90 minutes we will be at the top of the league I have no doubt."
Gareth Bale had been the star member of Madrid's front line most often sacrificed by Zidane in recent weeks as the Welshman was replaced in each of his last three outings.
However, Bale looked back close to the form which saw him shine towards the end of last season and at Euro 2016 and believes Ronaldo will also need time to get back to 100 percent fitness following his two-month injury layoff after the Euros.
"He's been working hard on his injuries since he came back," said Bale. "He hasn't had a pre-season like me and it takes a little bit of time."
Bale is yet to score since the opening day of the La Liga season, but insists the goals will arrive if Real continue to create the number of chances they did in the Canary Islands.
"We're not happy to lose four points, but if you look at the league overall we are in a good position," he added. "You have to look at the positives. Of course we are disappointed, but we are still unbeaten. We are still creating chances and if we keep doing that we'll score plenty of goals."