German midfielder Kroos was tipped to be rested for the midweek match after playing a lot of football in recent weeks, but Zidane has claimed that injuries to the likes of Luka Modric and Casemiro forced his hand.
"I had to play him because we were missing several players in that position," Zidane told reporters. "The plan was to give him a rest towards the end, but he wanted to play on until the end. I asked him and he said that he was feeling good and wanted to continue. It was a normal game for him."
La Liga leaders Real Madrid will return to league action with a trip to Alaves on Saturday afternoon.