The European Union on Thursday called for verification of each polling station result in the West African nation.
"It is important that all actors reject violence and call for calm. Any protest must be peaceful means to prevent the burning of the country; the police must react responsibly," EU foreign policy chief Federica Mogherini said in a statement.
Amid the violence, security forces stormed the headquarters of opposition leader and defeated presidential candidate Jean Ping.
Ping's supporters had been staging protests after official results gave Bongo a narrow victory in Saturday's presidential election, BBC reported.
Ping said two persons were killed as shots were fired.
His supporters accused the government of stealing the election.
The election result, announced on Wednesday, gave Bongo a second seven-year term with 49.8 per cent of the vote to Ping's 48.2 per cent -- a margin of 5,594 votes.
But Ping disputes the result in one province which show a 99.93 per cent turnout with 95 per cent voting for Ali Bongo.
Ping said the election was fraudulent and "everybody knows" he won.
He also denounced the raid which happened while he was not in the building.
Ping has called for international assistance to protect the population and has called for voting figures from each polling station to made public.
The US and EU have also called for the results to be made public while UN Secretary-General Ban Ki-moon has urged calm.
Ali Bongo took office in 2009 after an election marred by violence, succeeding his father Omar Bongo who had come to power in 1967.
Ping had been a close ally of Omar Bongo, serving him in ministerial roles and having two children with his daughter, Pascaline, a former Gabonese Foreign Minister herself.
