The case, revealing unsavoury tensions in a small French village, was one of the most famous faits divers, crime stories that became real-life soap operas, of the 1980s. Another murder was added when Jean-Marie Villemin, the father of four-year-old Gregory, shot dead a cousin who had been charged with the boy's murder, then released.
Yesterday's ruling by the Dijon appeals court put at least a formal end to suspicions surrounding Christine Villemin, the mother.
It had been expected after a prosecutor reported last year that inquiries had turned up no evidence to convict any killer. Henri-Rene Garaud, Mrs Villemin's lawyer, said the decision was 'a total rehabilitation' for his client.
The couple refused comment, saying they would remain silent until Mr Villemin goes for trial for shooting Bernard Laroche, his cousin. The case was moved to Burgundy from the Vosges where the original crime was committed because of the passions raised by the little boy's murder.
Gregory's bound body was found floating in the Vologne river on 16 October 1984, about four miles from the family home in the village of Lepange.
A low level of adrenalin found by the autopsy suggested that whoever tied him up and pulled a bonnet over his face before throwing him there had not frightened him and was probably someone he knew. The boy disappeared while playing outside the house, according to the testimony given by his mother.
Before the body was found, Gregory's uncle, Michel Villemin, said an anonymous telephone caller, known in French as a corbeau or 'crow', who had been pestering the family for three years with calls and anonymous letters, telephoned to say: 'I have taken revenge on the boss and I've kidnapped his son. I strangled him and threw him in the Vologne.'
There emerged a history of bad relations in the village, with rivalries and jealousy between various branches of the Villemin family. The father received a letter at work saying: 'I hope you die of grief, boss. It's not your money which will bring back your son.'
Suspicion in an investigation which was distinguished only by the lapses and ineptitude of the police and judges involved - the inquiry was handled by two police forces and three different examining magistrates - at first fell on Bernard Laroche, depicted as the poor relation of the Villemins.
Jean-Michel Lambert, the first examining magistrate who became known as le petit juge, 'the little judge', relying on evidence by a sister-in-law, charged Laroche with murder three weeks after the crime was committed.
When the sister-in-law retracted her evidence, Laroche was freed on 4 February 1985 but Jean-Marie Villemin, still convinced that his cousin had killed the boy, shot him dead with a hunting rifle on 29 March.
Christine Villemin was singled out as the next suspect after investigators concluded that some recordings of the 'crow' could have been a woman disguising her voice. The mother was charged with the murder in December 1986.
Maurice Simon, the second magistrate, took the case over in January 1987 and interviewed a total of 170 people. His inquiries swung suspicion back on the murdered cousin. A third magistrate, who took over when Mr Simon fell ill and retired, ordered handwriting analyses which found some similarity between Laroche's hand and that of the 'crow'.
In the meantime the Villemins, who now have other children, had to leave their village.
In the local cemetery, the inscription on Gregory's grave reads: 'Here lies an angel'.