He was arrested at a hotel along with fellow Fifa vice-president Alfredo Hawit, 64, on suspicion of accepting millions of dollars of bribes.
Uruguay FA chief Wilmar Valdez will replace Napout as interim Conmebol president until January.
Napout and Hawit, the interim president for North, Central America and Caribbean football, were among 16 current and former senior football officials indicted on 4 December by US authorities investigating corruption in the organisation.
The US Department of Justice alleges the 16 were involved in"racketeering, wire fraud and money laundering conspiracies "that saw them solicit and receive "over $200m (£132m) in bribes and kickbacks".
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