Zidane's men recovered from two goals down at Estadio de la Ceramica on Sunday to dramatically win 3-2, scoring three goals in the final 26 minutes.
Isco came off the substitutes' bench when the score was 2-0 – playing a part in two of the three Madrid goals – while Morata entered the field at 2-2 and scored the winner with seven minutes remaining.
Isco and Morata have only made 11 and seven league starts respectively this season and Zidane acknowledges that is something that needs to change.
"There is no doubt that Isco and Morata deserve to get more minutes," the Madrid boss told reporters.
"They did very well and changed the game for us. I'm certain that we will need to call on the whole squad.
"I gave Morata a couple of tactical bits of advice and told him he needed to be in the box to finish any chances and for him to stick on Bruno in the middle when we were defending.
"He got his goal and we are all happy. It was important for us to get the three points to remain top."
Zidane added: "At 2-0 down we had to change something. We did so and it worked out well for us. We made an attacking change and enjoyed more possession in their half.
"We knew that we were coming up against a good side, who have being doing fantastically well at home. We had to be patient and our substitutions ended up changing the game. "