Hugo Auradou and Oscar Jegou, who featured in France's 28-13 Test victory over Argentina on Saturday, were detained in Buenos Aires and will be taken to Mendoza where the crime allegedly took place.
"Today a commission from the province of Mendoza is travelling to Buenos Aires to bring them and proceed with doing the relevant examinations," said Martin Ahumada, a spokesman for the Mendoza prosecutor's office.
"If the examinations align with the testimony of the victim, the related charge will be made," he told AFP.
According to local media reports, the alleged attack took place at the Diplomatic Hotel in Mendoza, where France's players and staff were staying for last weekend's Test match.
Local prosecutors requested the immediate arrest of the two players following the allegation.
France are due to travel to Montevideo on Tuesday where they face Uruguay on Wednesday. The team is then due to return to Buenos Aires for a second Test against Argentina on Saturday.
"If the facts are proven, they are incredibly serious. You must spare a thought for the young woman," said French Rugby Federation (FFR) president Florian Grill.
"It's the opposite of everything that rugby is, of everything that rugby does, of everything that rugby builds... But you must let the investigation, which is necessary, take place," he told journalists.
Player in racism scandal
The arrests come a day after a racism scandal that saw France fullback Melvyn Jaminet ousted from the squad in Argentina.
Jaminet was removed after video of him making racist comments emerged on social media.
"I promise, the first Arab I see on the road, I'll headbutt him," Jaminet is filmed as saying in the Instagram video.
Toulon's Jaminet played seven minutes and kicked a penalty in France's first Test win over the Pumas on Saturday.
The FFR condemned his video comments as "totally unacceptable and against the fundamental values of our sport."
French Sports Minister Amelie Oudea-Castera praised the "rapid and appropriate response to the fear sparked" by the player's remarks, writing on social media platform X.
Jaminet subsequently apologised for his remarks after being booted out of the squad.
"I am deeply sorry and ashamed of my comments," Jaminet said on Instagram.
"Racism, in all its forms, is unacceptable and goes against everything I believe in.
"I understand the FFR's punishment and remain at their disposition to be able to shine a light on this incident."
