Bedoya had headed the federation since 2006 and was also one of the 11 members of the South American football federation's (CONMEBOL) executive committee. "Luis Bedoya Giraldo has submitted his irrevocable resignation for personal reasons as president and member of the executive committee of the Colombian Football Federation as of today," a statement said.
His resignation comes two weeks after the federation's accountant also resigned and with South American football reeling from the FIFA corruption scandal.
FIFA is embroiled in the worst scandal of its 111-year history, the United States having indicted several FIFA officials for bribery, money laundering and wire fraud in May.
CONMEBOL, an influential grouping that includes traditional football powers like Brazil and Argentina, is heavily embroiled in the corruption probe led by the U.S. Federal Bureau of Investigation (FBI).
Of 14 football officials and sports marketing executives indicted in the United States in May on bribery, money laundering and wire fraud charges involving more than $150 million in payments, eight were from South America.
U.S. Department of Justice allegations included one that three Argentine businessmen formed a company that entered into a $317.5 million contract with CONMEBOL to obtain exclusive worldwide commercial rights to the 2015, 2019 and 2023 Copa America tournaments, as well as a centenary cup next year.
Bribes of up to $110 million were promised to CONMEBOL officials, of which $40 million have already been paid, according to the U.S. indictment.
Bedoya, who a government source said had flown to the United States last Wednesday, was not named in the indictment and has always maintained his innocence.
The Colombian attorney general's office said they had opened an investigation into Bedoya and were sharing information with U.S. authorities. "We have spoken with North American authorities and they have a great interest on their part in collaborating with Colombia, although we cannot give more information," attorney general Luis Eduardo Montealegre told reporters.
(Writing by Andrew Downie; Editing by Peter Rutherford)
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