The 57-year-old FIFA vice-president was arrested in Zurich last week on a U.S. warrant accusing him of accepting bribes worth millions of dollars in connection with the sale of marketing rights to soccer tournaments in Latin America.
He is banned from all football activities and has agreed to be extradited to the United States.
"With the resignation of Mr Juan Angel Napout as president, the congress was convened for the election of officers (president and vice-presidents) for 26 January 2016," CONMEBOL confirmed in a statement on its website (www.conmebol.com).
Uruguayan FA chief Wilmar Valdez, who chaired the congress, has taken over as CONMEBOL president on an interim basis until the election.
Valdez said at the end of the congress on Friday that CONMEBOL, facing the worst crises in its history as it becomes embroiled in the U.S. investigation of corruption in FIFA, had focused on the reforms needed to restore public confidence in South American football.
Valdez, CONMEBOL’s fourth president since May 2013, did not detail the changes needed but said it was time that "money went where it was meant to, which is the clubs".
CONMEBOL was headed by Paraguayan Nicolas Leoz from 1986 until he resigned in 2013 when the net of investigations into corruption in the game began closing in.
Uruguayan Eugenio Figueredo took over but was among the first men arrested by FBI officers in Zurich last May in connection with the probe and Napout stepped in to replace him.
(Reporting by Ed Osmond in London; Writing by Rex Gowar; Editing by Alison Williams)
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