Darren Staples/Reuters Michael Platini (l) and Sepp Blatter (r) have been barred from all football activities on a national and international level.
In addition, FIFA also announced the suspensions of FIFA Vice-President Michel Platini, and FIFA Secretary General Jérôme Valcke, also for 90 days, and former FIFA Vice-President Chung Mong-joon for six years.
Valcke had already been put on leave last month pending an investigation into allegations that he sold World Cup tickets above face value.
The recommendation to suspend Blatter had been reported on Wednesday, however, the suspension of Platini came as a surprise and is significant. Platini was widely viewed as the most likely person to replace Blatter when a special election is to be held on February 26.
FIFA announced that the suspensions are effective immediately and are the result of pending investigations by the ethics committee. According to Paul Kelso of Sky News, the suspension of Blatter is "pending further investigation by Swiss prosecutors."
Last month, the Swiss attorney general announced that Blatter will face charges of "criminal mismanagement" and "misappropriation."
Among the charges is an allegation that Blatter gave a "disloyal payment" to Platini totaling 2 million francs ($2.1 million). That payment is alleged to have been made three months before Platini announced he would not run against Blatter in the 2011 FIFA presidential election.
While the 90-day suspensions will end prior to the presidential election in February - 90 days is the longest suspension that FIFA's ethics committee can hand down during a pending investigation - FIFA can extend the suspensions for an additional 45 days if needed.
If FIFA does extend Blatter's and Platini's suspensions, they could potentially be reinstated one week prior to the election, barring the conclusion of the investigations and any punishment handed down as a result of those.