The takeover ends the Bongo family dynasty's almost six decades in power and creates a new conundrum for regional powers who have struggled to find an effective response to eight coups in the area since 2020.
Central Africa's political bloc, the Economic Community of Central African States (ECCAS), condemned the coup in a statement, saying it planned an "imminent" meeting of heads of state to determine how to respond. It did not give a date.
Nigerian President Bola Tinubu, the current chair of West African bloc ECOWAS, said on Wednesday he was working closely with other African leaders to contain what he called a "contagion of autocracy" spreading across Africa.
Senior officers in Gabon announced their coup before dawn on Wednesday, shortly after an election body declared that Bongo had comfortably won a third term after Saturday's vote.
Later on Wednesday, a video emerged of Bongo detained in his residence, asking international allies for help but apparently unaware of what was happening around him. The officers also announced that General Brice Oligui Nguema, former head of the presidential guard, had been chosen as head of state.
The events follow coups in the past four years in Mali, Guinea, Burkina Faso, Chad and Niger, erasing democratic gains since the 1990s and raising concerns among foreign powers with regional strategic interests. The coups also showed the limited leverage of African powers once the military takes over.
ECOWAS threatened military intervention in Niger after a coup there on July 26 and imposed sanctions, but the junta has not backed down. Military leaders elsewhere have also resisted international pressure, such as in Mali. They have managed to hold on to power and some have even gained popular support.
Hundreds of people took to the streets of the capital of Libreville to celebrate Wednesday's coup in Gabon.
Bongo's popularity had worn thin amid claims of corruption, sham elections and a failure to spend more of Gabon's oil and mineral wealth on the country's poor. He took over in 2009 on the death of his father Omar, who had ruled since 1967.
The African Union, former colonial power France, the United States, Canada and Britain have all expressed concern about the coup. But they have not made direct calls for reinstating Bongo.
European Union's foreign policy chief Josep Borrell said on Thursday that Gabon's election had been full of irregularities. He said there was no plan to evacuate EU citizens.
A lack of international observers, the suspension of some foreign broadcasts and authorities' decision to cut internet service and impose a nighttime curfew after the poll raised concerns about the transparency of the vote.