The suspension was imposed following the allegedly non-consensual kiss Rubiales gave to Spain player Jenni Hermoso after this year's Women's World Cup final in which Spain beat England.
Rubiales said he will use his right to appeal, accusing FIFA of not giving him the chance to defend himself from.
"I will go to the last resort to see that justice is done and that the truth shines through," he said in a statement via social media.
The incident blew up into a sexism storm that attracted global headlines, overshadowing Spain's triumph. Rubiales is under investigation by Spain's High Court for alleged sexual assault and coercion following a criminal complaint by Hermoso.
"The FIFA Disciplinary Committee has banned Luis Rubiales 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," FIFA said in a statement on Monday.
Rubiales, who has the right to appeal, told Reuters that he would issue a statement via his social media accounts later on Monday, while his lawyers declined to comment on the decision.
The "Me Too" moment in Spanish football had been building for nearly a decade as the players tried to combat sexism and achieve parity with their male peers.
That included two dressing room rebellions that ended the international careers of several players.
They finally accomplished change thanks to an "exhausting" month-long standoff that ended in September when the RFEF agreed to make "immediate and profound changes" to its structure, according to the players.
FIFA's decision means Rubiales, 46, can no longer run for the RFEF presidency or General Assembly under Spain's new electoral regime for sports federations presented last month by the country's National Sports Council (CSD).
The CSD rules make ineligible anyone who has been sentenced by the disciplinary bodies of national or international federations or sports tribunals.
Rubiales resigned in September saying his position at the RFEF had become untenable. He had initially vowed not to stand down despite pressure from players, politicians and women's groups.
During his testimony to the court in the assault case, Rubiales denied Hermoso's accusations, according to the prosecutor's office. Rubiales has repeatedly said the kiss was consensual, while Hermoso says it was forced on her.
The investigating judge, who imposed a restraining order to prevent Rubiales from approaching Hermoso, also decided to expand the scope of the probe to include Jorge Vilda, the Spain squad's former coach who was sacked by interim RFEF president Pedro Rocha 10 days after FIFA suspended Rubiales from his post.
The coach was widely criticised for repeatedly applauding Rubiales during an emergency RFEF assembly in which the latter railed against "false feminism" and vowed not to resign.
"Mr Rubiales has been notified of the terms of the FIFA Disciplinary Committee’s decision today," FIFA said on Monday. "The decision remains subject to a possible appeal before the FIFA Appeal Committee."
