"The girl was handed over to her father in the town of Nyirszolos," embassy spokeswoman Irina Zvonova said. "All the documents drawn up by the French and Hungarian sides have been signed."
The mother, Irina Belenkaya, was arrested in Hungary while attempting to cross the border to Ukraine with her daughter Elise Andre on Sunday night.
The girl was held at the child protection center in Nyirszolos until she was handed over to her father, Jean-Michel Andre. They have now left the town.
Elise, who has dual Russian-French citizenship, was snatched from her 51-year-old father in southern France on March 20. The Frenchman was severely beaten in the incident, and said that his former wife was among the attackers.
The estranged couple has been embroiled in a "tug-of-war" for custody of their daughter for two years, with Russian and French courts siding with their nationals in the dispute. The girl has been abducted three times in two years.
Andre was awarded custody by a French court following the couple's divorce in 2007. After his former wife left the country, taking her daughter with her, a warrant for her arrest was issued in 2008.
Belenkaya was then awarded custody of Elise by a Russian court.
In response, Andre hired private detectives to trace his ex-wife and child, traveling to Moscow to seize his daughter and take her back to France. A Russian court subsequently issued a warrant for Andre's arrest.