Zidane asked Perez to keep Ronaldo last summer and to sell Bale as he began to shape his plans for the upcoming season in a meeting with the board.
Bale had fallen out of favour under Zidane after a series of injury problems.
He was left on the bench in the Champions League final in Kiev against Liverpool, and came on to score twice including a sensational overhead kick.
Bale said after the game that he was unsure on his future and that he would hold discussions with Real Madrid and his agent.
Zidane did not like this and decided that he wanted Bale to be sold.
But Perez ignored him, having broke the bank for the Welshman himself, he was desperate for Bale to prove his worth.
Instead he sold Ronaldo to Juventus which left Zidane furious.
The Frenchman was so disappointed with the decision that he decided to resign as boss.
“Zidane made it very clear when he decided to leave the club,” former president Ramon Calderon said.
“He insisted on keeping Cristiano and transferring Bale, and the president did completely the opposite.
“Zidane also wanted to sign some players and transfer others —apart from Bale— but he didn’t get his wish, so he decided to leave. And he was right.”
Real Madrid have paid the ultimate price this season for the decision to go against Zidane’s will.
They currently sit 5th in the La Liga table and are effectively already out of the title race.
Julen Lopetegui was sacked after his side were crushed 5-1 in El Clasico by Barcelona.
Santiago Solari has since been given the job on an 18-month contract but is unlikely to make it beyond the end of the season.