Military officers seized power in a coup on Wednesday minutes after an announcement that Bongo had secured a third term in an election, ending his family's nearly 60-year hold on power.
They placed him under house arrest and installed Gen. Brice Oligui Nguema as transitional leader.
The coup — West and Central Africa's eighth in three years —
drew cheering crowds onto the streets of the capital, Libreville. But the opposition, which says it is the rightful winner of Saturday's election, has raised objections.
"We were happy that Ali Bongo was overthrown but ... we hope that the international community will stand up in favor of the Republic and the democratic order in Gabon by asking the military to give back the power to the civilians," Alexandra Pangha, spokesperson for Alternance 2023 leader Albert Ondo Ossa, told the BBC.
She said that the junta's plan to inaugurate Nguema as head of state on Monday was "absurd."
Bongo was elected 2009, taking over from his late father who came to power in 1967. Opponents say the family did little to share Gabon's oil and mining wealth.
Before being detained, the Bongos lived in a luxurious palace overlooking the Atlantic Ocean. They own expensive cars and properties in France and the United States, often paid for in cash, according to a 2020 investigation by the Organized Crime and Corruption Reporting Project, OCCRP, a global network of investigative journalists.
Meanwhile, almost a third of the country's 2.3 million people live in poverty.
Military leaders ordered the arrest of several members of Bongo's cabinet early on Wednesday on accusations ranging from alleged embezzlement to narcotics trafficking.
State broadcaster Gabon 24 said on Thursday that duffel bags stuffed with cash wrapped in plastic have been confiscated from the homes of various officials. Its footage included a raid on the house of former cabinet director Ian Ghislain Ngoulou. He told the channel that the money was part of Bongo's election fund.
Full vote count
The coup in Gabon follows others in Guinea, Chad and Niger, plus two each in Mali and Burkina Faso since 2020. The takeovers have erased democratic gains in a region where insecurity and widespread poverty have weakened elected governments, worrying international powers with strategic interests at stake.
Alternance 2023 has said it wants a full vote count from Tuesday's election, which it said would show Ondo Ossa had won. Gabon's election commission said after the election that Bongo had been re-elected with 64% of the vote, while Ondo Ossa secured almost 31%. Ballot counting was done without independent observers amid an internet blackout.
Pangha said the opposition hoped to get an invitation from the junta to discuss the Central African country's transition plan but said it had not received anything yet.
The junta has not made its transition plans public.
The African Union's Peace and Security Council demanded on Thursday that the military refrain from any interference in the political process and called for fair and transparent elections. It said it will impose sanctions on the coup leaders if they do not return to barracks and restore constitutional order.