In a letter to the Uruguayan Football Association (AUF) the game's governing body said it would take over the day-to-day running of the AUF.
It also pledged to revise the association's statutes and adjust them to comply with those of Conmebol and FIFA, and when that process was complete, hold an election for president.
"The mandate of the regularisation committee will run until Feb 28, 2019," the letter, which was widely published in Uruguayan news media, said. "The regularisation committee will act as an electoral commission whose decision will be firm."
Neither FIFA nor the AUF responded to Reuters' requests for comment but Conmebol said the intervention "was based on the lack of guarantees for the electoral process."
The intervention came after "diverse interest groups in Uruguayan football expressed their concern over the lack of an electoral system with clear rules," Conmebol said in a statement.
Incumbent AUF president Wilmar Valdez unexpectedly resigned in July and the ballot to succeed him was postponed pending questions about the eligibility of the remaining candidates.
The lack of leadership means long-time coach Oscar Tabarez has not signed a new contract and his place has been filled temporarily by Under-20 coach Fabian Coito.
Coito will lead the side for next month's friendly match against Mexico in the United States.
With a population of only 3.5 million, Uruguay punches above its weight in global football. The nation won the World Cup in 1930 and 1950 and reached the semi-finals in 2010.
(Writing by Andrew Downie; Editing by Ian Ransom)
