Lucas Vazquez and Vinicius Junior were introduced after the break at the expense of Kroos and Isco and the double change proved to be decisive as Los Merengues went on to affirm a 1-0 win against their local rivals.
Vinicius was part of the build-up to the goal, he found Ferland Mendy with a perfect pass, before the Frenchman sent in a good cross for his compatriot Karim Benzema to slot past Jan Oblak.
Speaking to the media after the game, Zidane said he did not want to point fingers at Kroos and Isco for their poor first half display.
"I had to change things," the French coach said per a report from Marca.
"I wasn't happy with what I was seeing, but it wasn't the players' fault, it was mine.”
"I didn't want to point a finger at anyone, even less so at Isco and Toni, who are very good players.”
"I'm happy for the win, for all of the players, and everyone is happy with the result."
Real Madrid have now moved six points clear above rivals Barcelona, who play on Sunday against Levante at the Camp Nou.
