One of the two new victims was a policeman, the first member of the Gabonese security forces listed as killed in the violence sparked by the announcement on Wednesday of Bongo's victory in last weekend's election.
"I deplore the death of a police officer who was shot in Oyem," the main town in the north, Interior Minister Pacome Moubelet-Boubeya told AFP.
The attackers, who shot the policeman in the head, were arrested as they attempted to cross the border with Equatorial Guinea.
However the Gabonese capital has been without internet access since Wednesday.
Tension was also high in the economic capital Port-Gentil where a youth was shot dead by security forces overnight, according to witnesses.
"The parents wanted to march with the body up to the government building with many other people. They were dispersed by security and defence forces," one witness told AFP.
Several residents said the death was just one of several in Port-Bentil in recent days caused by the security forces.
Such claims have not been independently verified, but according to an AFP count the latest deaths bring the recent death toll to seven.
The archbishop of Libreville on today called on both the ruling party and the opposition to avoid an "imminent crisis".
Bongo was declared victorious by a razor-thin margin of just under 6,000 votes, but his main challenger Ping, a veteran diplomat and former top African Union official, has insisted the vote was rigged and yesterday claimed victory for himself.
"The whole world knows who is president of the republic, it's me Jean Ping," he said.
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