The 12-year-old girl, Baya Bakari, was found clinging to wreckage in the sea, hours after the crash.
She had been treated in hospital in the Comoros Islands for injuries thought to include a broken collar bone and burns.
The plane, going to the Comoros from Yemen's capital Sanaa, came down in bad weather with 153 on board.
Baya Bakari was accompanied on the journey back to France by the French Minister for Co-operation, Alain Joyandet, and other officials.
Her father, Kassim Bakari, met her on arrival and said he was "relieved but at the same time sad" to be with his daughter.
"I am happy I can see my daughter but at the same time, I lost my wife and it's not only my wife I mourn but for all the people who died in the crash," he said.
Doctors in the Comoros Island said Ms Bakari, who lives in Paris with her family, was "regaining her spirit and was in a satisfactory physical state", reported Reuters.
They said she had been discharged from hospital at the request of her father.
'Moral strength'
Speaking from Paris on Wednesday, Mr Bakari said his daughter had been thrown from the plane as it hit the water.
He said she clearly recalled the chaos of her time in the water, including hearing voices around her in the darkness.
"She's a very timid girl, I never thought she would escape like that," he said, adding that she was "fragile" and barely able to swim.
French officials in Moroni have praised the girl's courage, with Mr Joyandet describing her rescue as a "true miracle".
"She is a courageous young girl. She really showed an absolutely incredible physical and moral strength."
An uncle, Ali Abdou, who visited the girl in hospital in Moroni, told the BBC she did not yet know that her mother had died and had been told she was in another room.
The cause of the crash has not yet been identified but officials believe it is unlikely more survivors will be found.
Attempts are continuing to locate the plane and its black box flight recorders.
On Wednesday, a French government minister in the Comoros capital, Moroni, said that a detected signal thought to be from one black boxes was in fact a distress beacon.
Find out more about the black box
Ibrahim Abdourazak of the Comoros rescue centre told Reuters it was likely the victims' bodies were still inside the sunken plane.
"In two days we haven't found a body, any large pieces of debris or suitcases floating on the water," he said.
'Speculation'
There were 66 French nationals among the passengers. Most of the rest were Comorans, and most had flown on a different Yemenia aircraft from Paris or Marseille before boarding flight IY626 in Sanaa.
The EU and France have both said they highlighted safety concerns over Yemenia planes and said the jet that crashed had not flown into EU airspace since 2007.
The French transport ministry said on Tuesday that the Airbus 310 plane which crashed had been banned from France because of "irregularities".
Yemenia responded by criticising "false information and speculation about technical problems" on the plane.
The vice-president of the Comoros, Idi Nadhoim, also said France had not told them the plane was unsafe.
"It could have been easier for us if France had communicated to us the list of Airbus planes not good to fly, which is not the case," he told France 24 television.
Several Comoran expatriates angry with what they see as the poor state of the company's aircraft tried to stop passengers from checking in for another Yemenia flight leaving Paris Charles de Gaulle airport for Sanaa.
About 60 people failed to check in, reports said, but it was not clear how many did so as a result of the protest.
The French AFP news agency reported that the authorities were investigating whether a manslaughter case could be opened, but it was unclear against whom.
The crash was the second involving an Airbus aircraft in recent weeks. On 1 June an Air France Airbus 330 travelling from Rio de Janeiro to Paris plunged into the Atlantic, killing all 228 people on board.
