Genetic profiles of Sasha Ruseva and her husband, Atanas, matched that of the girl, said Svetlozar Lazarov, an Interior Ministry official.
Ruseva has said she gave birth to a baby girl four years ago in Greece while working as an olive picker, and gave the child away because she was too poor to care for her.
Maria has been placed in temporary care since last week after authorities raided a Roma settlement in central Greece and later discovered that girl was not the child of a Greek Roma couple she was living with. The couple has been arrested, and who have been charged for allegedly abducting Maria and document fraud.
A lawyer representing the Greek couple said Friday they planned to seek legal custody of the fair-haired girl.
The couple have told authorities they had received Maria after an informal adoption.
Under Greek law, child abduction charges can include cases where a minor is voluntarily given away by its parents outside the legal adoption process.
"Now that they're in prison there's not much they can do," their lawyer, Costas Katsavos, said.
"But provided what we said is borne out, that it was not an abduction, then logically they will be released from prison and they will be able to enter a proper (adoption) process ... They truly and ardently want her back."
Costas Yannopoulos, director of the Greek children's charity "Smile of the Child" which has been looking after the girl said he had no comment on her fate.
"We are dealing with the humanitarian side of this issue, looking after a young girl," Yannopoulos told the AP in response to the news.
Maria's case has drawn global attention, playing on the shocking possibility of children being stolen from their parents or sold by them. But its handling by media and authorities has raised concerns of racism toward the European Union's estimated 6 million Gypsies - a minority long marginalized in most of the continent.
Paphitis reported from Athens, Greece. Associate Press writer Derek Gatopoulos in Athens, Greece, contributed.