Real Madrid president Perez had been appointed as the chairman of the competition, which was announced with 12 founding teams and to widespread criticism on Monday (AEST).
Perez spoke on Monday about a need to change football, with clubs struggling financially in the wake of the COVID-19 pandemic, while he also cited a lack of interest in the game from younger generations.
Yet his words did little to appease the furore and, on Tuesday, the six English clubs involved in the competition all pulled out amid pressure from the Premier League, Football Association (FA), UEFA and the UK government.
The owners of Liverpool, Manchester United, Arsenal and Manchester City all offered apologies to their fans for their part in the plans.
Atletico Madrid, Inter, Milan and Juventus subsequently pulled out on Wednesday, albeit Perez has claimed the latter two remain committed.
Yet Perez insists he will not let the proposals die, and is adamant that there must be drastic reform to football, maintaining the European Super League was put together as a plan to save the game.
Speaking on the El Laguaro radio show following Madrid's win over Cadiz, Perez said: "We were working last night until late. We have been working many years on this project. We have not explained it very well, perhaps.
"They have not given us a chance either. Some do not want anything to happen. It cannot be that in England, the six lose money, and 14 make money. In Spain the top three lose money, and the others make money. It cannot continue – at the moment the rich are those who are losing money.
"I am a bit sad, disappointed. We have been working three years on this project, on fighting the current financial situation in Spanish football. You cannot touch LaLiga, so you look for more money midweek and the Champions League format is obsolete.
"I have never seen aggression greater on the part of the president of UEFA, it was orchestrated, it surprised us all. Insults and threats, as if we had killed football.
"We are just working on saving football. We have worked very hard on something that would satisfy everyone.
"There was a campaign, totally manipulated, that we were going to finish the national leagues. That we were ending football, it was terrible. But we were working for football to survive.
"If you think the Super League is dead, you're absolutely wrong."
Perez was also bullish in the face of UEFA and FIFA's condemnation.
"Reality is reality. Look at the TV records, and how many people watch big games, and how many people watch the other games. We have to be real," he said.
"That new Champions League format in 2024 has no meaning. No one can understand it. We need a new format to create more money. Young fans don't watch football, they have other hobbies.
"I talk to [Joan] Laporta, Barcelona are still with us. Juventus did not leave. I'm not scared of FIFA or UEFA."
Concluding, Perez also stated that no club would be able to afford major signings at the end of the season.
"It's impossible to make signings like [Kylian] Mbappe and [Erling] Haaland without the Super League," he said. "Not just for us, there will be no big signings, for any club, without the Super League.
"When I took over, Madrid could not pay its players. We changed the world with the Galactico signings. Now after COVID-19, things have to change again."