The court in the western city of Nantes granted an heiress of the Omar Bongo Ondimba the right to details of Ali Bongo's birth in the latest twist in an ongoing controversy over his wealth and whether he has the right to stand for reelection in 2016.
The judgement is "legally incontestable", even if "diplomatically complex", lawyer Eric Moutet said, welcoming the decision.
Last year French author Pierre Péan alleged that Ali Bongo was of Nigerian origin and adopted during the 1967-70 Biafran war, a claim that "was not a scoop", he told RFI at the time.
Péan also claimed he had lied about his educational qualifications.
Ali Bongo says he was born in Brazzaville on 9 February 1959.
If the allegations prove true, his inheritance of much of his father's wealth could be contested.
More seriously still his presidency would be in breach of Gabon's constitution, which bans people who have adopted Gabonese nationality from standing for president.