The sanction comes after Rubiales refused to resign from his position after becoming embroiled in a scandal at the 2023 Women's World Cup in Australia.
Rubiales kissed Jenni Hermoso on the lips during Spain's post-match celebrations and claimed it was "consensual" even though the player said she "did not enjoy it."
Hermoso has since issued a statement to explain the kiss was "never consensual" and added she has been under "constant pressure" to justify Rubiales' behaviour.
The Spanish FA have issued a statement questioning Hermoso's version of events and insisting Rubiales "has not lied" about the incident.
FIFA have now taken action and confirmed Rubiales has been sanctioned for 90 days and disciplinary proceedings have been opened.
"The chairman of the FIFA Disciplinary Committee, Jorge Ivan Palacio (Colombia), in use of the powers granted by article 51 of the FIFA Disciplinary Code (FDC), has decided today to provisionally suspend Mr. Luis Rubiales from all football-related activities at national and international level," FIFA confirmed in a statement.
"This suspension, which will be effective as of today, is for an initial period of 90 days, pending the disciplinary proceedings opened against Mr. Luis Rubiales on Thursday, August 24."
FIFA have also banned Rubiales and members of the RFEF from contacting Hermoso until a decision on the incident has been taken.
"Likewise, the chairman of the FIFA Disciplinary Committee and in order to preserve, among other factors, the fundamental rights of the national soccer team player Ms. Jennifer Hermoso and the good order of the disciplinary proceedings before this disciplinary body, has issued two additional directives (article 7 FDC) by which he orders Mr. Luis Rubiales to refrain, through himself or third parties, from contacting or attempting to contact the professional player of the Spanish national football team Ms. Jennifer Hermoso or her close environment.
"Likewise, the RFEF and its officials or employees, directly or through third parties, are ordered to refrain from contacting the professional player of the Spanish national team Ms. Jennifer Hermoso and her close environment."
There has been an outpouring of support for Hermoso after Rubiales announced he would not be resigning during an explosive press conference.