Protesters shouting "Ali must go!" tried to storm the offices of the election commission shortly after authorities announced his re-election by a narrow majority.
Security forces used tear gas and stun grenades to push several hundred protesters back.
Bongo won 49.80 of the vote against 48.23 percent for his rival Jean Ping, or a razor-thin 5,594 votes of a total 627,805 registered voters, Interior Minister Pacome Moubelet-Boubeya.
Bongo, whose father held onto power for four decades, sought relection after winning a first term in 2009 in a poll that was marred by violence.
Any appeal by Ping would be likely to focus on disputed results in one of the country's nine provinces - the Haut-Ogooue, the heartland of Bongo's Teke ethnic group.
In Saturday's vote, turnout was 59.46 per cent nationwide but soared to 99.93 per cent in Haut-Ogooue, where Bongo won 95.5 per cent of votes.
"It's going to be difficult to get people to accept these results," one member of the electoral commission confided to AFP, asking not to be named because of the sensitivity of the subject.
Opposition delegates in the electoral commission boycotted a vote to approve the results on Wednesday and they have vowed to fight for a recount.
As fears rose of a contested result and violence, the electoral commission and Bongo came under pressure from fellow politicians and the international community to deliver a fair outcome.
"The European Union repeats the call made by the head of its observer mission that results should be published for each polling booth," a spokeswoman for EU foreign policy chief Federica Mogherini said in a statement.
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