French media reported looting and rioting in the city of Port Gentil in the heart of the central African nation's oil producing zone, with one local resident saying prisoners had been freed from a local jail.
"This is just what happens in Africa," Angel Nzeg, a female opposition supporter in Libreville said of the chaos surrounding the poll announcement. "What do you want us to do?" she said.
Ex-defence minister Ben Bongo, 50, scored 41.73 percent of the vote, the interior ministry said on state television, ahead of ex-interior minister Andre Mba Obame and third-placed Pierre Mamboundou. Both had claimed victory in Sunday's poll and said they would protest against the outcome.
Ben Bongo rivals accuse him of rigging the result to ensure a transfer of power from his father, who brought stability during nearly 42 years of rule but faced accusations he used petrodollars to enrich family and friends.
"This is a victory for the Gabonese people. Ali Ben Bongo has won it. I salute his courage because at the beginning nothing would have suggested he was going to win," Communications Minister Laure Olga Gondjout told reporters.
In Port Gentil, an unnamed resident was quoted by French state radio France Info as saying prisoners freed from a local jail roamed the streets and had set fire to a petrol station.
Security forces earlier used tear gas to disperse hundreds of opposition supporters who had led an overnight sit-in on a square near the election commission in the capital Libreville.
Observers and financial markets have played down the risk of major instability in the tiny country but some unrest was expected given the dispute over the result.
"The result is not unexpected, Ali Ben Bongo had seemed to be groomed by his father, but there has been a groundswell of opposition. There is definitely a sense on the ground that people didn't want to see a Bongo dynasty," said Kissy Agyeman-Togobo of IHS Global Insight.
Assuming order is restored, little change was expected in the business-friendly policies espoused by the late president.
"We would expect his policies to be broadly in line with his father's, so relatively friendly to foreign investors, both in the financial sector and oil industry. It's relatively good news for foreign businessmen and investors," said Richard Segal, a specialised debt broker with Knight Libertas.
Gabon hosts oil firms including France's Total and U.S.-based Vaalco, and is one of the few sub-Saharan countries to have launched a Eurobond.
Analysts say Ben Bongo now faces the challenge of diversifying the economy to replace revenue from Gabon's dwindling oil reserves.
