They said they feared the official results were being massaged to ensure a dynastic succession from father to son, an accusation the former defence minister denies.
"Gabon is a republic and not a kingdom. This country has decided that power cannot be passed from father to son. It's crazy," one opposition supporter said.
Observers and financial markets have played down the risk of major instability in the central African oil nation, but some unrest was expected given the dispute over the result.
Witnesses said anti-riot police and gendarmes armed with tear-gas launchers watched the protesters while a helicopter hovered overhead.
Land and sea borders have been closed in Gabon and text messages were blocked by at least one telephone operator.
Election commission officials had said they expected an announcement of the result on state television late on Wednesday but that appeared to switch to Thursday.
Ali Bongo is favourite to win in a country that has secured years of foreign investment in its oil industry but largely failed to improve the lives of most citizens.
Yet his claims of victory have been matched by rivals Andre Mba Obame, a former interior minister, who resigned in July, and Pierre Mamboundou, one of the few candidates with no history of ties to Bongo.
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.
Libreville residents said the situation across most of the city remained calm on Thursday.
Omar Bongo's death in June, aged 73, ended nearly 42 years of rule that brought stability to Gabon.
Gabon hosts oil firms including France's Total and US-based Vaalco, and is one of the few sub-Saharan countries to have launched a Eurobond.
Analysts say any successor to Bongo will face the challenge of diversifying the economy to replace proceeds from its dwindling oil reserves.