The Frenchman took full responsibility for the heavy defeat, but appeared perplexed by their display after a strong start at the Mestalla.
Karim Benzema fired them ahead in the 23rd minute, but the first of three penalties enabled Valencia to level and they never looked back.
"We started the first half-hour well," Zidane, as quoted by AS, told reporters.
"After the goal we fell apart and changed the dynamics. Everything happened to us; three penalties, an own goal. It is difficult to understand."
Lucas Vazquez conceded the first spot-kick, which Carlos Soler scored at the second attempt - the video assistant referee ordering a retake.
Raphael Varane then chipped past Thibaut Courtois in bizarre fashion at the end of the first 45 to compound the champions' misery before it got even worse after the break.
Marcelo and Sergio Ramos gave away penalties, both of which Soler dispatched to ensure he took home the match ball, and Valencia were able to inflict the joint-biggest defeat of Zidane's managerial career with Madrid.
"There is no justification or excuses," the 48-year-old added.
"I don't think Valencia has been tactically better than us. The only thing is that we started well and everything changed after the goal.
"This is difficult to understand but yes, the one most responsible is me. We must find solutions after the goal they scored."
Ex-Watford boss Javi Gracia, who had little money to spend this summer and instead turned to the club's academy, insisted the victory was for everyone who works at the Mestalla.
He told Plaza Deportiva: "I feel very happy, but above all for my players for what they have gone through without reward.
"Winning today in such a forceful way reinforces us all, the coach as well.
"I am happy, yes, for offering this victory to so many people who work at the club, to the veterans who come to give encouragement. These things are not forgotten and I am excited to share these three points with them."
The win ended Valencia's four-match streak without success to see them rise to ninth in the table while Madrid are four off leaders Real Sociedad in fourth position.
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