Lopetegui's replacement would be announced "soon", added Rubiales.
"We have a group of players who have been together for two years to work towards the World Cup and I have been sporting director, so I understand the motivation is huge".
Sport insist the other 22 players were disappointed with the coach because he had told them all to focus on the national team and not to think about their futures at club level.
MI made a decision to fire Frieder immediately and promoted assistant coach Steve Fisher, who led the 3-seeded Wolverines to the national title.
But that's exactly what Spain has done by firing manager Julen Lopetegui on Wednesday, the day before the massively important tournament was scheduled to kick-off in Russian Federation.
"I've been at all the training sessions, in the day-to-day we've been present and I can't change anything in these two days".
"I very much admire Julen and respect him greatly".
Lopetegui, who last month signed a contract extension with Spain until 2022, admitted was disappointed not to have the chance to lead his country at the World Cup but defended his conduct in negotiations with Madrid.
Almost 30 years ago, MI faced nearly the same situation as Spain when coach Bill Frieder announced before the NCAA tournament that he would leave after the season to take over Arizona State.
The Spanish Football Association reportedly believed it would be inappropriate for Lopetegui to continue his tenure, considering he only informed the Spanish FA of dealings with Real just minutes before the official press release from the mega-club.
Rubiales inferred he felt Lopetegui's decision to join Madrid so close to the start of the tournament "obliged" him to take drastic action.
"It is true that there is very little time to prepare, but the moment is here and we are clear about what we want to achieve", he said.
Lopetegui, 51, was appointed Spain's coach in July 2016 and never tasted defeat in the job, leading the team through 20 unbeaten games ahead of the World Cup.