Cécile Bourgeon, the mother of the child, elicited nationwide sympathy with her tale of how, pregnant at the time, she had fallen asleep on a park bench in May and had woken to find her little girl was gone.
The 25-year-old had issued a tearful appeal for help in finding her daughter, Fiona.
But both Bourgeon and her partner Berkane Maklouf, 32, were taken in for questioning on Tuesday and told investigators that the girl had died at home, prompting a police search.
The mother has been charged with four offences: failing to help a person in danger, unlawfully handling a dead body, falsely reporting a crime and interfering with a crime scene.
Arriving separately to be charged at the Palais de Justice in Clermont-Ferrand on Thursday evening, both Bourgeon and Maklouf were greeted by angry crowds.
In this video taken by Centre France, a mob screams "whore" and "bitch" as they charge towards the police vehicle transporting Bourgeon.
According to investigators, Bourgeon and her partner gave conflicting accounts of how Fiona died.
Maklouf said the child died after choking on her own vomit and that the couple panicked when they found her body in the morning.
A judicial source said Bourgeon had cracked under intensive questioning and told police that Fiona had died as a result of being hit repeatedly by her boyfriend after a heavy drinking session, and that her body had been stuffed in a leather bag, and then buried naked on the fringes of a forest.
About 40 police officers with three sniffer dogs were called in to scour the edge of a lake south of the central city of Clermont-Ferrand to search for the body. The search is set to resume on Friday, with French media reporting that Maklouf has indicated that he is willing to help officers find the girl's body.
On Thursday, Bourgeon had attempted to lead police to the sport where Fiona was interred, but also explained that it was Maklouf himself who had physically buried her, and that her recollections were vague.
If convicted, Maklouf could face up to 30 years in prison. His lawyer said he has denied the charge.
On May 16th, Bourgeon appeared before French media, tearfully asking the French nation for help in finding her daughter.
“I think about everything and nothing in particular. This is very hard, psychologically," she said in a separate interview. Here is a short video of first national television appearance (in French.)
In August The Local reported how the Bourgeon had renewed her desperate appeal for help and even spoke to the media of her disappointment at the lack of solid leads in the search for her daughter.
“Three months have already passed and still no good news,” she told told regional daily La Montagne. “We’re still waiting for a solid lead. It’s very hard, but I have to keep fighting,” she added.
“Where I’ve been disappointed is that there have been so many testimonies which have led nowhere. But if someone does have information, they must come forward,” Bourgeon said.
The realisation that the couple had lied for the last four months has left those who led the search for Fiona disgusted.
“What they have done is despicable. It’s horrible, indefinable and inhuman,” Stephane Pozzo told Europe1 radio.