In a statement on Monday, Álvaro Morata, César Azpilicueta, Rodrigo Hernández and Marco Asensio on behalf of the entire team, said the women’s team had been “tarnished” after Mr Rubiales kissed Jenni Hermoso.
The statement, read at a press conference, said: “We want to reject what we consider to be unacceptable behaviour on the part of Mr Rubiales, who has not been up to the standard of the institution he represents.
“We place ourselves firmly and clearly on the side of the values that sport represents. Spanish football must be an engine of respect, inspiration, inclusion and diversity and must set an example with its behaviour both on and off the field.”
The team also expressed its “pride” and “most sincere congratulations” to the women’s national team for winning the World Cup final in Sydney against England.
It was during celebrations at the end of the game when Mr Rubiales grabbed Spanish player Jenni Hermoso’s head and kissed her on the lips in a moment broadcast to live television.
The men’s team added: “A historical milestone loaded with meaning that will mark a before and after in Spanish women’s football, inspiring many women with an invaluable victory.
“For this reason, we want to regret and express our solidarity with the players who have seen their success tarnished.”
The statement comes as Mr Rubiales was suspended by FIFA from “all football-related activities at national and international level” for an initial 90 days while an investigation continues.
He has doubled down on his defence of the kiss, claiming it was a consensual act, which Ms Hermoso disputes.
He said: “At no time was there any aggression, indeed, there was not even the slightest discomfort, but an overflowing joy in both.”
Mr Rubiales also said he had support online and in the streets.
Spain’s Sport Administrative Tribunal (TAD) on Friday opened a case against Mr Rubiales for “serious misconduct”.
Rubiales’ behaviour has sparked outrage in Spain and abroad with hundreds turning out to protest in Spain’s capital, Madrid, last week.