Gabon's incumbent President Ali Bongo has won a closely fought presidential election, the country's interior ministry has announced.

Interior Minister Pacome Moubelet Boubeya said on Wednesday that Bongo had obtained 49.80 percent of Saturday's vote, beating rival candidate Jean Ping who received 48.23 percent.

Bongo won by only 5,594 votes, of a total 627,805 registered voters.

Election commission members belonging to the opposition immediately denounced the result, with one commissioner for Ping's party, Paul Marie Gondjout, saying the vote had been "stolen".

"They say [Ping's camp] they will not accept this result at all," Al Jazeera's Catherine Soi, reporting from the capital Libreville, said.

Moments after the announcement, anti-government protests erupted in parts of Libreville.

"Protests have started [and] are expected to continue," Al Jazeera's Soi said, adding that clouds of smoke and tear gas could be seen over parts of the city where clashes were taking place.

"Jean Ping has been telling his supporters not to accept a vote that is not favourable to him ... He is telling his people to defend their vote, to defend their choice," Soi said.

"They say that they have been cheated."

READ MORE: Jean Ping lays claim to Gabon presidency win

Security forces used tear gas and stun grenades against protesters shouting "Ali must go!", who tried to reach the headquarters of the election commission, AFP news agency reported.

'Never seen results like these'

Presidential elections are held in a single round in Gabon, with the candidate with the most votes winning outright. The constitutional court now must finalise the provisional results.

Any appeal by Ping would be likely to focus on disputed results in one of the country's nine provinces - the Haut-Ogooue, where Bongo won 95.5 percent of the vote. Results from the province showed a turnout of more than 99 percent, compared with a nationwide turnout of 59.46 percent.

"It's going to be difficult to get people to accept these results," one member of the electoral commission told AFP, asking not to be named because of the sensitivity of the subject.

"We've never seen results like these, even during the father's time," he added.

Opposition delegates in the electoral commission boycotted a vote to approve the results on Wednesday and they have vowed to fight for a recount.

A spokesman for Bongo's campaign, Alain-Claude Bilie-By-Nze, called the vote "free, democratic and transparent", according to the Associated Press news agency.

Second term

Bongo, 57, has now won a second term as head of the tiny oil-rich state, previously ruled for 41 years by his father, Omar.

In 2009, Bongo was declared winner of the presidential election after his father's death. The result was disputed and in the ensuing clashes several people were killed, buildings looted and the French consulate in the economic capital Port-Gentil was torched.

Prior to becoming Bongo's bitter rival, Ping, a 73-year-old career diplomat well known on the international scene, worked with Bongo senior for many years.

Before the interior ministry's announcement, the European Union, which monitored the election, renewed a call for Gabon to publish "detailed results" for every polling station, urging all actors to help keep peace.

"We invite all stakeholders to exercise restraint, work to maintain civil peace in the post-electoral context and make use of legal channels to resolve any dispute," the EU said.