The bearded multimillionaire, the face of North American football for two decades, pleaded guilty to racketeering, part of a massive US corruption case targeting world football's governing body.
FIFA on Tuesday admitted that it had processed a $10 million payment from South Africa to a disgraced football official but denied the world body's secretary general Jerome Valcke was involved.
FIFA said a former finance committee chief who died last year, Argentine Julio Grondona, authorised the 2008 payment which went to Jack Warner.
Warner, one of 14 people facing corruption charges in the United States over $150 million in bribes, was at the time Grondona's deputy on the finance committee.
FIFA released a statement after the New York Times reported that Valcke, right hand man to FIFA leader Sepp Blatter, had signed off on the payment.
Despite the denial, Britain's Press Association news agency reported a letter from South Africa's Football Association chief to Valcke which indicated he knew about the payment.
The South African government asked FIFA to "withhold" money intended for the organisers of the 2010 World Cup and send it to a development project in the Caribbean run by Warner, the FIFA statement said.
According to US investigators, the $10 million was a bribe promised to Warner and his deputy Chuck Blazer to secure the 2010 World Cup.
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