Carvajal was making his first appearance for Madrid since 3 January but lasted just 28 minutes before sustaining an apparent injury to his right thigh.
He has been restricted to 12 games in all competitions this term and is now considered a big doubt for the Champions League last-16 first leg with Atalanta on 25 February (AEDT).
The Spain international joins the likes of Sergio Ramos, Eder Militao, Alvaro Odriozola, Eden Hazard, Rodrygo, Federico Valverde and Marcelo on the sidelines.
Madrid boss Zidane is concerned about the long list of injuries he has had to contend with this term and is unsure why so many players have been ruled out of action.
"There are a lot of injuries," he said. "I'm worried because when you lose a player it bothers me. It's a relapse [for Carvajal].
"I'm sorry for him because he was fine to play and is a very important player to us. But I can't explain all these injuries."
Asked if the packed fixture schedule is to blame, with Madrid playing nine times since the turn of the year, Zidane said: "I'm not going to get into that.
"We already have enough trouble. The calendar is what it is. We didn't have a normal pre-season and there are many injuries.
"I hope to get my players back but I'm not going to get involved in the rest."
Lucas Vazquez replaced Carvajal at right-back and slotted in seamlessly by teeing up Kroos for Madrid's second, 30 minutes after Karim Benzema had opened the scoring.
Kroos, who scored and assisted a goal in the same Madrid match for the first time since November 2018, joined Zidane in bemoaning his side's injury nightmare.
"It worries us a lot, of course. We are without important players," he said. "Dani has come back from three injuries in a row - it's not right, we don't like it.
"But the others have to do as much as possible. We can't change the situation, just accept it."
Valencia managed just one attempt on target at Estadio Alfredo Di Stefano - Maxi Gomez's shot from range - in what was a routine third successive league win for Madrid.
Zidane's men have now kept back-to-back clean sheets and the Frenchman is pleased with the improvement made by his side at the back.
"That much is evident," he said. "We believe a lot in what we do. We are overcoming difficulties and there is a lot left for us to give."
Madrid, which has now gone 13 home LaLiga matches without losing to Valencia, is five points adrift of Atletico Madrid having played two games more than the league leader.
But two-time title-winning boss Zidane is not yet giving up hope of chasing down rivals Atletico, which Madrid faces at Wanda Metropolitano on 8 March.
"We are going to continue doing what we are doing," he said. "We are not going to look at what others are doing. Today we played a very good game.
"They all defended very well without the ball and when got forward we caused a lot of damage. We have to continue in this way."
Valencia head coach Javi Gracia has won only one of his eight LaLiga games against Madrid and took full blame for his side's lacklustre display in the Spanish capital.
"It was a bad game from us," he said. "I do not know if it was our worst of the season but one of the worst. The intention was to be more aggressive, it was very easy for them.
"The coach has the maximum responsibility in everything. This is a step backwards in our trajectory. From the first minute we have not been able to demonstrate anything.
"We have not seen options to achieve anything positive here. We could not even link two passes"