Alejandro Dominguez wants to restore Conmebol's credibility after being unanimously elected to replace Juan Angel Napout as president.
Dominguez was the only candidate standing after interim president Wilmar Valdez withdrew from the race.
Napout stepped down in December after being arrested as part of the investigation into FIFA corruption.
Dominguez, who will also assume Napout's place as a FIFA vice-president, said he is intent on restoring the damage done by the scandal.
"We cannot fail to recognise that we are in a time of crisis and we know the responsibility of what it means taking over the presidency of Conmebol, but we are confident that together we will be able to restore the credibility of the confederation, with the emphasis on transparency in our management," Dominguez said in his first address following his election.
"Conmebol is currently enduring a bad institutional period, we are sure of this, but we are starting a new era in which everything will be done with transparency and clarity. [We will] establish control systems that helps our accounts to be up to date and which will prevent any individual or private entity to profit over the interests of football.
"Fair play on and off the pitch will be the flagship of this new stage we begin today with the support of all the South American leadership."
Dominguez was elected president of the Paraguayan Football Association in November 2014, also succeeding Napout in that role when his compatriot took the confederation's top job.