The already-suspended chief sent his resignation to the federation's interim president, he said in an open letter, and also explained his decision to eventually step down in a television interview.
"I'm going to (resign), yes, because I cannot continue my work," Rubiales told television show Piers Morgan Uncensored.
"(Family and friends) say to me 'Luis, you need to focus on your dignity and continue your life. If not you are going to damage people you love and the sport you love.'"
Rubiales, 46, sparked a worldwide backlash after forcibly kissing midfielder Jenni Hermoso during the medal ceremony following Spain's World Cup triumph in Sydney on Aug. 20.
After he refused to resign FIFA provisionally suspended him for 90 days, while Spanish public prosecutors filed a lawsuit against him for sexual assault and coercion earlier this week.
Hermoso, 33, had filed a complaint at the National Court on Tuesday, formally accusing Rubiales of sexual assault.
In an open letter published by Rubiales on Sunday night, he said he had informed the federation he was also stepping down as a vice-president of European football governing body UEFA.
"After the swift suspension carried out by FIFA, plus the rest of the procedures opened against me, it is evident that I will not be able to return to my position," said Rubiales in the letter.
"Insisting on waiting and clinging to it is not going to contribute to anything positive, neither for the federation nor for Spanish football.
"Among other things, because there are powers that be that will prevent my return."
Rubiales, who insists the kiss was consensual, said he did not want Spanish football to be hurt by "such a disproportionate campaign" against him.
"I have faith in the truth and I will do everything in my power so that it prevails," he wrote.
Rubiales said his departure would contribute "stability" to the 2030 men's World Cup bid in which Spain is involved.
The chief's mother Angeles Bejar went on a hunger strike in protest against the treatment of her son, locking herself in a church on Aug. 28.
However, two days later she was taken to hospital because she was feeling unwell.
"My daughters, my family, and the people who love me have suffered from the effects of excessive persecution, as well as many falsehoods," added Rubiales in his letter.
"But it is also true that on the street, more and more every day, the truth is prevailing."
Spanish politicians quickly responded to Rubiales' decision.
"The feminist country is advancing faster and faster," said second deputy prime minister Yolanda Diaz on social media platform X (formerly Twitter).
"The transformation and improvement of our lives is inevitable. We are with you, Jenni, and with all women."
Spain's equality minister Irene Montero wrote "It's Over" on X, a slogan used by Hermoso and her fellow players in protest against Rubiales.
Over 80 players went on strike from the women's side in protest after Rubiales' fierce defensive speech following the incident, in which he railed against "false feminism" and said he would not step down.
The players said they would not return until the leadership of the RFEF (Spanish football federation) was changed—controversial women's coach Jorge Vilda was sacked last week.
The RFEF, under interim president Pedro Rocha, also apologized for the "totally unacceptable behavior" of Rubiales.
Vilda's former assistant Montserrat Tome is the new coach—it is the first time a woman has led the team.
Spain's women's team is due to play Nations League matches against Sweden and Switzerland on Sept. 22 and 26 respectively.
Meanwhile, Spanish prosecutors' lawsuit against Rubiales will be analyzed by a National Court judge.
If the judge accepts the request, a magistrate will be assigned to head an investigation which will end either with a recommendation for the case to go to trial or be dismissed.
Hermoso, who plays for Mexican club Pachuca, has said the unwanted kiss had left her feeling "vulnerable and like the victim of an assault," with a statement on social media describing it as "an impulsive, macho act, out of place and with no type of consent on my part."
She has also accused Rubiales of pressuring her to speak out in his defense immediately after the scandal over the kiss erupted, which prosecutors said could be considered a crime of coercion. (AFP)