Bongo and his main rival Albert Ondo Ossa lead a race of 14 candidates vying for the top job in the small oil-rich central African state, in an election the opposition claimed was hit by organisational "chaos".
The 64-year-old incumbent Bongo took office in 2009, succeeding his father Omar, who died after more than 41 years in power.
Onda Ossa -- a 69-year-old economics professor who served as a minister under Bongo from 2006 to 2009 -- was chosen by the main opposition grouping, Alternance 2023, as its joint candidate just eight days before the election.
An AFP journalist saw dozens of people waiting at voting stations in the centre of Libreville, though most streets, decked out in the colours of Bongo's governing party, were unusually empty for a Saturday.
After polls closed, the government announced that internet would be suspended until further notice, and said it was imposing a nightly 7:00 pm-6:00 am curfew from Sunday August 27.
Communications Minister Rodrigue Mboumba Bissawou said on public television that the move was necessary to "counter the spread of calls for violence...and false information".
'Elements of fraud'
Earlier Saturday, the opposition accused the Bongo government of deliberately creating a disorganised election.
Onda Ossa's team said he was only able to cast his vote after his polling station opened eight hours behind schedule.
His communications manager Guy-Pamphile Mba told AFP the delay at the polling station in the centre of Libreville was apparently due to an absence of voting equipment.
Francois Ndong Obiang, president of Alternance 2023, told AFP many others had experienced similar delays.
He also claimed that ballots listing Ondo Ossa's name were missing in some polling stations, and criticised authorities for creating "chaos".
Ondo Ossa said in a live video on the Facebook page of Alternance 2023 that Bongo had increased the "elements of fraud".
The Gabon election authorities did not comment when contacted by AFP, but a special advisor to the president said on X, formerly Twitter, that the "fake news machines" were running at "full speed".
Shortly ahead of the elections, a storm erupted over a purported conversation between Ondo Ossa and a fellow opposition figure.
The conversation -- recorded without the pair's knowledge and disseminated on social media -- refers to various strategies "to create a power struggle" and support from other countries.
Bongo has accused the pair of treason, saying the remarks reflect a plot to take over with the help of "foreign powers".
At an eve-of-election rally in Libreville, Bongo charged that the two sought to "destroy this country".
Alternance 2023 this week issued a statement strongly denying the "veracity and authenticity of this conversation" and accusing the government of "shameful manipulation".
As well as electing a president, Gabon's 850,000 voters will be choosing candidates for the legislature and local councils.
In the days leading up to the ballots, the main opposition parties had already cried foul over a last-minute change to voting rules in the legislative race, which they say violated the separation of powers.
The new move stipulates that any vote for a local deputy will automatically be a vote for that deputy's presidential candidate.
Critics said the move would lead to an "unfair vote", favouring the ruling Gabonese Democratic Party (PDG) since Ondo Ossa is not backed by any single party.
Ondo Ossa has told AFP that if elected: "I will dissolve parliament and convene new elections" for the body.
For years, Bongo, who once had ambitions to be a funk singer before being groomed for politics, struggled in the shadow of his charismatic father.
In 2016, he was narrowly re-elected with just 5,500 more votes than his rival, who claimed the election had been fixed.
The announcement of the results sparked violence in the capital Libreville that left five dead, according to the government.
The opposition says 30 people were shot dead by the security forces.
In October 2018, Bongo suffered a stroke that sidelined him for 10 months.
His prolonged absence stoked claims he was unfit to rule effectively and fuelled an attempted coup.
He returned to work after his convalescence bent on showing himself to be a man of rigour, keen to root out "traitors" and "profiteers" in his inner circle.
Visitors and diplomats say that Bongo today is mentally acute but has mobility problems in his right arm and leg.
In recent months, he has been busy with foreign trips and a nationwide tour to defend his record and pitch himself as an agent of change.
Yet foreign journalists have been largely restricted from covering the election, with the France-based Reporters Without Borders (RSF) denouncing an "infringement of media pluralism".