During the campaign, Bongo pledged change in the impoverished West African nation, while also defending the legacy of his father, who had been widely accused of corruption.
"It's not contradictory - not at all," he said as he attended his final campaign rally on Saturday.
"How could I not be confident?" Bongo asked, pointing at the thousands of supporters chanting his name.
Gabon is sub-Saharan Africa's fourth biggest oil producer, the world's third biggest provider of manganese and Africa's second biggest wood exporter, but an estimated 60 per cent of the population lives below the poverty line.
Bongo and the other frontrunners Andre Mba Obame and Pierre Mamboundou have all promised a fairer distribution of the country's natural resources.
A total of 23 politicians were originally in the race, but Cassimir Oye Mba resigned from the race on Sunday afternoon, saying that he was worried the polls outcome would trigger violence.
Other candidates, including Jean Eyeghe Ndong, a former prime minister and Paul Mba Abessole, a former opposition leader, decided to stand down on Friday in favour of Obame, a former interior minister.
But the announcement also caused a row with four other contenders, including Oye Mba, a former oil minister, denying claims that they had joined the other candidates in pulling out of the race.
Many candidates have questioned the electoral roll, saying that the official figure of 813,164 eligible voters in a country of 1.5 million was too high.
However, Adama Gaye, an Africa analyst based in Senegal, said that the election was likely to be the most open in Gabon's history.
"President Bongo was not just Africa's longest-serving president, but also the world's longest-serving president," he told Al Jazeera.
"Because of his really high stature and financial muscle the elections were usually a foregone conclusion and there was also support from the French authorities to ensure he won."
More than 300 observers were accredited for the vote, including representatives from the African Union, the Organisation of the Islamic Conference and a global grouping of francophone countries.
|Despite tight security in the capital, many have left the city for fear of violence [AFP]
Opposition candidates have warned that they will not take a Bongo victory lying down, our correspondent said, and there are fears that a win by Bongo could ignite lingering anger over the huge personal fortune accumulated by his father.
Despite tight security in the capital, many people have been leaving the city and heading to their rural homes, he added.
A group of leading intellectuals in Gabon on Saturday urged all sides not to resort to violence after the election, pointing to "numerous worrying signals" and warning of "confrontations" in the wake of the vote.
And before the polls opened, Bongo issued a warning to any potential protesters.
"It is clear that we cannot accept disorder... We shall use all the institutions that the law authorises us to use - the street belongs to no one," he told Radio France International.