The sport's governing body provisionally suspended Rubiales for 90 days following his unsolicited kiss during the medal ceremony after Spain won the Women's World Cup in Sydney on August 20.
FIFA said Rubiales had broken its code of conduct and would now be banned from all football activities for three years.
Rubiales responded by announcing he will appeal against the ban.
"I am announcing as of now that I will be appealing," Rubiales wrote on X, formerly known as Twitter.
"I will go as far as taking the case to the highest court to ensure that justice is done and that the truth comes out," he added in a post which also included a 'flexed biceps' emoji.
Hermoso said the incident left her feeling "vulnerable and like the victim of an assault" and described it as "an impulsive, macho act, out of place and with no type of consent on my part".
Rubiales, who repeatedly insisted the kiss was consensual, resigned as head of the Spanish football federation in September.
"The FIFA disciplinary committee has banned Luis Rubiales, the former president of the Spanish Football Association (RFEF), from all football-related activities at national and international levels for three years," the Zurich-based organisation said in a statement.
FIFA said Rubiales had been notified of the decision on Monday and had 10 days to request a so-called motivated decision, which if requested, would be published on FIFA's legal website.
"The decision remains subject to a possible appeal before the FIFA Appeal Committee," the statement said.
"FIFA reiterates its absolute commitment to respecting and protecting the integrity of all people and ensuring that the basic rules of decent conduct are upheld."
Widespread ramifications
The case of the kiss has had widespread ramifications in Spain, leading to a shakeup of the management of the women's team and sparking demonstrations by feminist and student groups.
After Spain beat England 1-0 in the World Cup final, the RFEF initially put out a statement quoting Hermoso as saying the kiss was "a natural gesture of affection and gratitude".
Rubiales offered a cursory apology but later toughened his stance in his defiant speech to a meeting of the federation on August 25, prompting Hermoso to issue her own statement denying that the kiss was consensual and saying it had left her feeling "vulnerable" and like "the victim of an assault".
A day later, the federation accused her of "lies" over the incident, threatening legal action against her.
The coach of the World Cup-winning team, Jorge Vilda, who had enjoyed the full support of Rubiales when his authoritarian methods were questioned last year, was fired and replaced by a woman, Montse Tome.
Reports in Spain said Vilda had demanded to check players' shopping bags and made the squad leave their bedroom doors open during team training camps to ensure the players were still there in the evenings.
Despite the removal of Rubiales and Vilda, the players of Spain's national women's team expressed their concerns that the federation's approach was not changing fast enough by threatening to strike.
Hermoso returned to action for the national team on Friday and scored the winner in the 1-0 Nations League victory against Italy.
Afterwards she said: "I can tell you (I thought about) many things, but life sometimes gives you little gifts, and today I thought about a lot of people behind me this time.
"I am happy because, thanks to them, today I enjoyed football once again."