In a statement, Rubiales said his position had become untenable, with the Spanish football federation later confirming he had sent a resignation letter to acting president Pedro Rocha.
A Spanish prosecutor last week filed a complaint with the high court against Rubiales for sexual assault and coercion over his allegedly unsolicited kiss on the lips of player Jenni Hermoso.
The complaint, announced on Friday, describes how Rubiales kissed Hermoso on the mouth “without her consent” while holding her head with both hands after Spain defeated England to clinch victory in the World Cup final in Sydney on August 20.
Rubiales has described the kiss as mutual and consensual, and had until Sunday defied calls from players, government officials and others for him to resign.
Hermoso last week lodged a criminal complaint against the 46-year-old.
Rubiales had been suspended for three months from all football activities by FIFA, pending an investigation by soccer’s world governing body into his actions.
“After the rapid suspension carried out by FIFA, plus the rest of the proceedings opened against me, it is clear that I will not be able to return to my position,” Rubiales said in his statement.
“Insisting on waiting and clinging … is not going to contribute anything positive, neither to the Federation nor to Spanish football.
“Among other things, because there are de facto powers that will prevent my return.”
He said he had also stepped down as a vice president of European soccer body UEFA.
Jenni Hermoso, Spain’s all-time top scorer with 51 goals, has yet to comment on Rubiales’ resignation.
The case has sparked outrage among players and many in wider Spanish society.
“The feminist country is advancing faster and faster,” Spain’s acting labour minister Yolanda Diaz posted on social media on Sunday in reaction to Rubiales’ resignation.
“The transformation and improvement of our lives is inevitable. We are with you, Jenni, and with all women.”
Rubiales continued to defend his version of events.
“I have faith in the truth and I am going to do everything in my power to make it prevail,” he said in his statement.
In an interview with journalist Piers Morgan on Sunday Rubiales added he made the decision to resign having talked with family and friends.
“Luis, you have to focus on your dignity and continue your life. (Otherwise) you will probably be hurting more people you love and the sport you love,” he quoted them as saying.
