Joining him, the French president's predecessor, Jacques Chirac, was also booed, according to AP news agency.
Dozens of onlookers yelled: "We don't want you - leave" and "No to France".
But the two men were reportedly applauded inside the palace as they laid wreaths at the foot of Mr Bongo's coffin, which was draped in Gabon's national flag.
The former colonial power has close economic and political links to Gabon, with around 1,000 troops stationed in Libreville, where French energy firm Total is an investor.
In his last months, Mr Bongo's relations with Paris were soured by a French investigation into allegations of embezzlement.
Two other African leaders who are the focus of the same inquiry, Denis Sassou-Nguesso of the Republic of Congo and Teodoro Obiang Nguema of Equatorial Guinea, were due to attend Tuesday's funeral in Libreville.
Gabonese reporter Linel Kwatsi, in the capital, told the BBC there had been anger among Mr Bongo's supporters in Gabon at the time over the Paris corruption inquiry and French media coverage.
The presidents of Benin, Burkina Faso, Burundi, Cameroon, the Central African Republic, Chad, Democratic Republic of Congo, Mali, Senegal, Sao Tome and Togo were also on the guest list.
Foreign dignitaries passed in front of Mr Bongo's coffin at the presidential palace, where it was taken last Thursday to lie in state.
Ali-Ben Bongo (centre) may not be the only contender to succeed his father
Thousands of Gabonese lined up at the palace over last few days to pay their respects.
The late president's 50-year-old son Ali-Ben Bongo, who is Gabon's defence minister and a favourite to succeed his father, said in a eulogy: "For more than 40 years you were our light," reported AP.
"We, your children, your family, we take a solemn vow to keep the flame alive."
After the prayer service the coffin was moved outside for a two-hour military parade in the capital's Independence Square.
Also present for the ceremony was African Union Commission President Jean Ping, a Gabonese who some analysts have speculated could be a contender in the forthcoming presidential election.
Rose Francine Rogombe took over as interim head of state last week and has 45 days to organise polls in the West African nation.
It emerged last month Mr Bongo was being treated in a Barcelona clinic, amid unconfirmed reports he had cancer.
The government said on Monday of last week that the 73-year-old had died of a heart attack.
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