Spanish FA chiefs were left furious following Lopetegui being announced as Real Madrid boss, and the decision was made tonight to fire him, despite their first World Cup game being just two days away.
With Julen Lopetegui being announced as the new Real Madrid manager, speculation is rife as to who will take over in the national team hotseat.
Rubiales accused Lopetgui of betraying the federation's values.
In the first reaction to the decision, former Spain forward Juanito said Rubiales' arguments had been impeccable. Last month, Lopetegui agreed to extend his contract with the national team through 2020.
The World Cup kicks off on Thursday when host nation Russian Federation plays Saudi Arabia at the Luzhniki Stadium in Moscow.
Lopetegui is yet to lift any club trophy as a manager, but won the UEFA European U19 Championship in 2012, and the UEFA European U21 Championship a year later.
"I admire Julen a lot, I respect him a lot, I think he's a top trainer and that makes it more hard to make the decision". "Winning is important, but above that, we need to know how things have to be handled".
Spain, the 2010 winners, are third favorites to win this year's competition, according to bookmaker SkyBet.
Spain begin their World Cup campaign against Portugal on the 15th of June, followed by matches against Iran and Morocco on the 20th and 25th respectively. Every possible candidate would have been a little risk, because nobody will win 3 Champions in a row like Zidane.
Rubiales has already left his impression after taking over a federation which was in the hands of embattled official Angel Maria Villar for almost three decades.
When Diego Maradona was sent home after testing positive for a banned drug during the 1994 World Cup, Argentina never recovered and were knocked out by Romania in the second round. He got the money reimbursed and spent only about 500,000 euros ($590,000) with new travel arrangements for sponsors and federation officials.
Quoting Lineker's tweet, Fabregas went one stage further, jokingly (we hope) suggesting Lopetegui's dismissal may see him receive a late call-up to the squad.