Bensouda claims this will be a preliminary examination to determine if there is enough evidence for a full inquiry.
The news came only days after President Ali Bongo, re-elected by a wafer-thin margin in the August 27 vote over his rival Jean Ping, vowed to form "an inclusive government" for the oil-rich central African country.
Chief prosecutor Fatou Bensouda said Libreville had referred the violence to her office on September 21, asking it "to open an investigation without delay."
Violence initially erupted on August 31 after Bongo was first declared the winner of the elections. Opposition demonstrators set parliament ablaze and clashed with police, who made hundreds of arrests.
Opposition figures say more than 50 people were killed. The government has given a toll of three dead.
Ping declared himself "president-elect" and asked for a recount in one province.
In the letter of referral to the ICC signed by Gabon's Justice Minister Denise Mekamne Edzidzie, the government accuses Ping and his supporters of incitement to genocide and crimes against humanity.
It highlights a speech which Ping gave during his electoral campaign, in which he allegedly called on his supporters to "get rid of the cockroaches."
"These words were an incitement to commit the crime of genocide," the letter says.
Among the other accusations of crimes against humanity the Gabonese authorities allege the ransacking and torching of government buildings and instructions given to individuals "to fire on the crowds, and take part in creating a climate of violence and terror among the civilian population."
They also allege acts of torture in Ping's campaign headquarters where "one person was tied up and the victim of inhumane and degrading treatment, his feet were pierced with nails."
But Ping's lawyer Emmanuel Altit told AFP the letter to the ICC from the Gabonese authorities was a "response to our own investigations which show probable cause of crimes against humanity."
"They only allege preparations to commit crimes. We have been investigating actual crimes.There's a difference."
"Several dozen civilians have been killed", he said, adding the opposition's dossier of investigations would be sent to Bensouda "in the near future" and would "complement her own inquiries".
In what will be a lengthy process, Bensouda said her office will "be conducting a preliminary examination".
This was "not an investigation," she cautioned, but would examine all the information to see if there is enough evidence for a full inquiry.
"I must consider issues of jurisdiction, admissibility and the interests of justice in making this determination," she said in a statement.
Gabon is a signatory to the tribunal's founding guidelines set out in the Rome Statute. And it acknowledged in its letter that its actions could also be open to investigation.
Bongo's family has exercised a long grip on power in Gabon with Ali Bongo taking over from his father Omar Bongo, who ruled for four decades, after his death seven years ago.
Bongo was installed for a second time as president on Tuesday, three days after the Constitutional Court dismissed Ping's claims of fraud.
But his second mandate has received a cool reception from the African Union and the United Nations, while the European Union voiced regret the vote count had not been transparent.