Last week Xavi criticised the Portuguese coach's style of football and declared he "has left no legacy for the future", while Iniesta said the new Chelsea manager had "damaged Spanish football" due to his confrontational style.
In his three years at Madrid Mourinho was the main antagonist in the rivalry between the two biggest clubs in Spain, most famously poking then Barcelona assistant coach Tito Vilanova in the eye after a match in August 2011.
Mourinho won Madrid's first league title for four years in 2012.
Mourinho hit out at Iniesta during his unveiling at Stamford Bridge on Monday, saying: "I damaged Spanish football by being the coach who broke Barcelona's dominance."
And Perez, speaking during an interview with Marca TV, concurred with the 50-year-old's assertion.
"I understand why Xavi and Iniesta are angry with Mourinho, they haven't beaten us in any of the last five games," he said. "It's not a good strategy to criticise your opponent when you don't win."
Referring to Mourinho's comments, Perez then added: "Mourinho ended Barca's period of always beating Madrid, he was right when he said that."
Mourinho won three trophies in total during his tenure at the Bernabeu while Barca won seven in the same period and Catalan midfielder Cesc Fabregas was quick to laugh off the former Porto manager's comments.
"Madrid ended our hegemony?" he told radio station Onda Cero. "We have just won the league by 15 points."
Fabregas also said that he wants to fight for his place at Camp Nou.
The Catalonia native has not enjoyed the happiest of times since his move from Arsenal in 2011, struggling to hold down a regular place in the starting line-up and occasionally being booed by sections of the crowd.
Fabreags, 26, has been linked with a return to the Premier League, with Manchester United being touted as possible suitors, but Fabregas has moved to quell that talk, insisting he is not distracted by paper rumours.
"It has taken a lot for me to get where I am, and I am not thinking about throwing it all away for nothing," he added.
"If Barcelona said that they didn't want me, that would be another thing - but what I truly want is to triumph at Barcelona. That's been my dream since I was a kid."
Uefa ban of Malaga upheld by Court of Arbitration
Spanish club Malaga will not be able to take their place in next season’s Europa League after the Court of Arbitration for Sport (CAS) rejected the club’s appeal of a Uefa ban from continental competition.
Uefa, European football’s ruling body, which is getting tough on teams that live beyond their means, initially banned Qatar-owned Malaga for two years in December because of overdue payments to other clubs and Spanish tax authorities.
That was later reduced to a year after the club “regularised its overdue payables” and they appealed to CAS asking for the Uefa decision to be annulled or replaced with less-severe sanctions.
However, CAS rejected the appeal and ruled that Malaga, who finished sixth in La Liga last season, will also have to pay the original fine of €300,000 euros (Dh1.41 million).
Malaga’s Europa League place will be taken up by Rayo Vallecano, who finished eighth in La Liga.
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