Lopetegui was announced as Zinedine Zidane's successor in a move that surprised many just days before the World Cup in Russian Federation is due to start.
The Spanish football federation (RFEF) explained it had dismissed the 51-year-old because the negotiations with the European champions occurred "without any information to the RFEF". "But the players and new coaching staff are going to do everything they can to take the Spanish national as far as they can".
Rubiales said firing Lopetegui was not the best solution for the national team but it was needed after being caught by surprise by Real Madrid's announcement.
However, the decision angered the Spanish FA, with Rubiales adding: "I don't want to get into how Real Madrid should go about things".
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"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".
Spain begin their campaign to regain the trophy from holders Germany on Friday evening, when they take on Portugal, with Russian Federation and Saudi Arabia set to open the tournament on Thursday afternoon.
Now removed from his position, reports on Wednesday morning suggested Spain's Under-21 coach Albert Celades would be an option to step in for the World Cup. We will touch the staff as little as possible, as soon as we have something to communicate, we will do it. "Maybe this is tough now, but in the end it will make us stronger". I found out with a phone call five minutes before the official announcement.
"He told us five minutes before the press release", Rubiales said.
Hierro is an obvious replacement for Lopetegui, due to his prior involvement in the Spain set-up.
Rubiales said the players, who Spanish media said had tried to dissuade him from such drastic action, had vowed to give everything for the team. We know we have a a great chance, that's what I have transmitted to them. Spain will take on Euro 2016 winners Portugal in what promises to be one of the ties of the group stages.