FIFA's ethics committee has provisionally banned Sepp Blatter, Michel Platini and Jerome Valcke for 90 days in the wake of a Swiss criminal investigation.
FIFA presidential candidate Chung Mong-joon has also been handed a six-year ban.
It had been widely reported on Wednesday that FIFA president Blatter was set to face the sanction, while news of UEFA president Platini's impending suspension was also leaked to the media.
Platini, a candidate for the FIFA presidency in February's emergency election, issued a statement on Thursday morning accusing the governing body of "an attempt to damage my reputation."
Blatter and Platini will now not be involved in any football activity for the next three months while investigations continue. The 90-day suspension can also be extended by a further 45 days.
Blatter's lawyer has said the FIFA president "did not engage in any misconduct, criminal or otherwise," with the Swiss "disappointed" that the ethics committee did not give him a chance to be heard and looking to clear his name.
FIFA secretary general Valcke, who had already been released from his duties after allegations relating to World Cup ticket sales, has been handed the same suspension.
With Blatter suspended, FIFA confirmed that African leader Isaa Hayatou gets automatically elevated to the top job by virtue of being the longest-serving vice president on its executive committee. He will serve as acting president of the governing body for the next 90 days.
The 69-year-old Hayatou, who has ruled African football for 27 years, said on Thursday that he will not be a candidate for the Feb. 26 presidential vote.
International Olympic Committee president Thomas Bach said "enough is enough'' at FIFA and has called for a "credible external presidential candidate'' to take over.
Bach said FIFA "cannot continue to remain passive" and "must act swiftly to regain credibility'' for the organization and the sport. Bach said FIFA has a "structural problem'' that "will not be solved simply by the election of a new president."
Bach says FIFA must "accelerate and deepen the reform process'' and "should also be open for a credible external presidential candidate of high integrity, to accomplish the necessary reforms and bring back stability and credibility to FIFA."
A FIFA statement on the 90-day bans said: "The adjudicatory chamber of the Ethics Committee chaired by Hans Joachim Eckert has provisionally banned FIFA President Joseph S. Blatter, UEFA President and FIFA Vice-President Michel Platini, and FIFA Secretary General Jerome Valcke (who has already been put on leave by his employer FIFA) for a duration of 90 days.
"The duration of the bans may be extended for an additional period not exceeding 45 days."
Should it be extended by 45 days, that would see the provisional suspension end on Feb. 20 -- only six days before the election of Blatter's successor is due to take place -- meaning a disciplinary hearing would have to take place before that time.
The pair can appeal against the suspension to FIFA's appeals committee within two days of being notified of the decision but they will remain suspended at least until the appeal is held.
The New York Times reported that Blatter filed an official appeal on Thursday night through a letter sent by his lawyer to the head of FIFA's ethics committee.
According to the Times, Blatter's lawyer demanded a hearing as well as access to the committee's case file. The appeal reportedly says Blatter should not be suspended until he is proven guilty in the Swiss investigation.
The appeal also criticised the committee for not making Blatter aware of his suspension before releasing the news publicly.
Blatter's lawyers had said they would expect the "ethics committee would want to hear from the president and his counsel, and conduct a thorough review of the evidence, before making any recommendation to take disciplinary action."
That does not need to be the case for a provisional suspension, however.
FIFA ethics rules state: "The chairman of the adjudicatory chamber may make his decision on the basis of the case files available to him, without hearing the parties, in which case the parties shall be summoned to a hearing or invited to submit written statements after the decision has been issued.
"After hearing the parties, the chairman of the adjudicatory chamber shall confirm, revoke or amend his decision."
FIFA's statement said that Blatter, "for the duration of the 90-day ban, is not allowed to represent FIFA in any capacity, act on the organisation's behalf, or communicate to media or other stakeholders as a FIFA representative."
FIFA vice president David Gill and fellow executive committee member Wolfgang Niersbach have called for an emergency meeting of FIFA's ruling body to be held.
According to a statement from the English Football Association, of which Gill is vice chairman, the FA said "there will be a meeting of the 54 UEFA nations as soon as next week.''
The FA was one of the first federations to endorse Michel Platini's candidacy for FIFA president, and the English are not withdrawing that backing yet.
"At the FA board meeting last week, we decided that remained our position while inquiries into certain allegations were being investigated,'' the FA said. "We now await the results of both the ethics committee inquiry and the investigation of the Swiss attorney general."
The UEFA executive committee issued a statement supporting Platini in a move that defied FIFA as European football's governing body said on Thursday it would not invoke statues requiring its highest-ranking vice president, Angel Maria Villar, to be appointed acting president.
UEFA said "this is because the UEFA executive committee is aware that the UEFA president will immediately take all necessary steps to appeal the decision of the FIFA ethics committee to clear his name.''
The UEFA statement stressed that the executive committee "expressed its full confidence" in Platini and will meet next Thursday in Nyon. All 54 UEFA member associations will meet at UEFA headquarters on the same day.
Chung, meanwhile, has been handed a six-year suspension from all football activity.
The South Korean, who this week vowed to sue to Blatter for embezzlement, had previously said he was anticipating a lengthy ban.
The statement added: "The former FIFA Vice-President Chung Mong-joon has been banned for six years and fined CHF 100,000. During this time, the above individuals are banned from all football activities on a national and international level. The bans come into force immediately.
"The grounds for these decisions are the investigations that are being carried out by the investigatory chamber of the Ethics Committee. The chairman of the chamber is Dr. Cornel Borbely. The investigation into Joseph S. Blatter is being carried out by Robert Torres, the investigation into Michel Platini by Vanessa Allard.
"The proceedings against the South Korean football official Chung Mong-joon were opened in January 2015 based on findings in the report on the investigation into the bidding process for the 2018/2022 FIFA World Cups.
"He has been found guilty of infringing article 13 [General rules of conduct], article 16 [Confidentiality], article 18 [Duty of disclosure, cooperation and reporting], article 41 [Obligation of the parties to collaborate] and article 42 [General obligation to collaborate] of the FIFA Code of Ethics.
"The Ethics Committee is unable to comment on the details of the decisions until they become final, due to the provisions of article 36 [Confidentiality] of the FIFA Code of Ethics."
Valcke's lawyer, Barry Berke, said the Frenchman was the subject of "false allegations."
Information from the Press Association was used in this report.