According to Argentina's migration authorities, Bolsonaro boarded a private plane in the northeastern city of Puerto Iguazú on Tuesday evening, just 40 minutes after crossing into the country by land.
Argentina's foreign ministry has denied that Brazil requested an explanation over Flavio Bolsonaro's transit through the country on his way to the United States.
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The denial comes after a Brazilian diplomatic source told AFP on Friday that Brazil had summoned Argentina's diplomatic representative to "provide explanations" about Bolsonaro's journey.
According to the source, who spoke on condition of anonymity, the meeting took place in Brasília on Thursday and was described as a "routine procedure".
On Wednesday, Brazil's defeated right-wing presidential candidate Flavio Bolsonaro arrived in Miami after crossing into Argentina with his family and boarding a private plane bound for Ecuador, according to Argentine authorities.
The private plane that eventually took Bolsonaro to the United States following his surprise election defeat was paid for by an intermediary using a US bank account, the head of the airline told AFP.
Relations between Brazil and Argentina have been strained since July, when Brasília recalled its ambassador and downgraded diplomatic ties with Buenos Aires following repeated insults from Argentine President Javier Milei, who described Brazilian President Luiz Inácio Lula da Silva as "a thief" and "corrupt".
Bolsonaro lost Sunday's presidential runoff to left-wing incumbent Lula da Silva, despite having led the first round of voting earlier this month.
Bolsonaro, who received tacit support from US President Donald Trump, is under investigation in Brazil for alleged corruption, money laundering and tax evasion.
He was ordered to surrender his passport and is expected to lose his parliamentary immunity following his election defeat.
Despite his defeat, he insisted on Wednesday that he was Brazil's legitimate president after fleeing to Florida in self-imposed exile.