Rubiales has been under fire since he kissed Spanish national team star Jennifer Hermoso after Spain’s women took World Cup gold in Australia and New Zealand.
The suspension comes into effect from today and for the next 90 days and covers all national and international football.
FIFA opened a disciplinary case against Rubiales on Thursday.
Rubiales himself believes that the kiss was consensual with Hermoso and announced on Friday that he will not resign from his post.