Violence continued for several days after President Ali Bongo was declared reelected at the end of August.
Clashes broke out shortly after the announcement that Bongo had beaten opposition leader Jean Ping and the opposition said more than 50 people were killed by the security forces.
The investigation in France started in April 2017, following a legal complaint by a French-Gabonese citizen in September 2016.
He was arrested on the night of 31 August 2016 when masked men attacked Ping's headquarters and claims there was a "night of horror" during which dozens of people were wounded or killed.
The inquiry was not originally into charges of crimes against humanity but into alleged arbitrary arrest, torture, acts of barbarism and attempted assassination.
But in June the judge added crimes against humainty to the charge sheet.
"The investigative judge considers that at first glance it was not possible to skip crimes against humanity," the plantiff's lawyer, William Bourdon, told RFI.
"There are some strong, convincing elements" in the case, he added. "In respect of his French citizenship, this allows, as you know, a French judge to recognise its [France] own judisdiction"
The International Criminal Court earlier this month sent a team to investigate the post-election violence.