The U.S. Justice Department and Federal Bureau of Investigation did not immediately respond to requests for comment following Blatter's announcement
Blatter initially attempted to bat away the furore, relying on his network of friends to hold onto power at FIFA, which he joined in 1975.
In a presidential election Friday, Blatter held off sole challenger Prince Ali of Jordan 133-73 in the first round of voting, prompting Ali to pull out of a subsequent second round.
On Tuesday, Prince Ali declined to say if he'd run again, but didn't rule it out. "I am at the disposal of all the national associations who want a change, including all of those who were afraid to make a change," he told CNN.
Michel Platini, the president of European body UEFA who had called for Blatter's resignation last week, priased his decision today to go.
"It was a difficult decision, a brave decision, and the right decision," said Platini, Blatter's one-time protege.
Meanwhile the probe into alleged corruption at FIFA continues. Blatter was not mentioned in either the U.S. or Swiss investigations and his resignation appeared to do little to change that fact as of Tuesday.
Switzerland's office of attorney general reiterated that it was not investigating the outgoing FIFA president.
“Joseph S. Blatter is not under investigation by the OAG. His announced resignation will have no influence on the ongoing criminal proceedings,” the attorney general said in a brief statement.
The investigation however closed in on those around Blatter on Tuesday, when FIFA was forced to deny that his right-hand man, Secretary-General Jerome Valcke, was implicated in a $10 million payment that lies at the heart of the U.S. case.
But at the same time, a letter addressed to Valcke was published outlining the transaction.
The organization said in an earlier statement that Valcke, who has been secretary-general since 2007 and is seen as one of the most powerful men in world sport, had no role in the payments, which were authorized by the chairman of FIFA's Finance Committee.
The chairman of the committee at the time of the payments was Argentina's Julio Grondona, who died last year.
A person familiar with the matter said on Monday that U.S. prosecutors believe Valcke made the $10 million bank transactions which are central to a U.S. bribery investigation against FIFA.
Al Jazeera and wire services