Rubiales kissed Spain forward Jenni Hermoso on the lips following her side's 1-0 win over England in the Women's World Cup final in August.
The 33-year-old says the kiss was not consensual and she later filed a legal complaint against Rubiales, who eventually stepped down from his post in September.
On Monday, FIFA announced the three-year ban for breaching article 13 of its disciplinary code and now the disgraced former president says he will appeal against the punishment.
"I am announcing as of now that I will be appealing," Rubiales wrote on X, formerly Twitter.
The 46-year-old, who refused to apologise for his actions, added: "I will go to the last resort so that justice is done and the truth shines. Due to the many efforts of some politicians, media and institutions, the disproportion and injustice committed is becoming increasingly clear."
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Hermoso, who said her image had been tarnished by the kiss, returned to the national side in October and scored an 89th-minute winner against Italy.
Rubiales has also been facing a criminal investigation in Spain after prosecutors filed Hermoso's initial complaint of sexual assault with a court in Madrid and added a second of coercion - the latter relates to alleged pressure on the player to defend the disgraced official against the backlash from his actions.
Rubiales appeared in court last month, where he denied both offences but was slapped with a restraining order that means he cannot go within 200 metres of Hermoso. World Cup-winning manager Jorge Vilda, who was sacked in September, is also being investigated as part of the criminal case against Rubiales.
FIFA's statement explained: "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, having found that he acted in breach of article 13 of the FIFA Disciplinary Code.
"This case relates to the events that occurred during the final of the FIFA Women’s World Cup™ on 20 August 2023, for which Mr Rubiales had been provisionally suspended for an initial period of 90 days.
"Mr Rubiales has been notified of the terms of the FIFA Disciplinary Committee’s decision today. In accordance with the relevant provisions of the FIFA Disciplinary Code, he has ten days in which to request a motivated decision. The decision remains subject to a possible appeal before the FIFA Appeal Committee.
"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."