Ndong Sima, a 68-year-old economist, served as prime minister under Bongo from 2012 to 2014 before becoming a critic and eventually challenging him unsuccessfully in elections in 2016 and 2023.
His appointment was made in a decree by the new military leader, General Brice Oligui Nguema, who was sworn in as interim president on Monday after the coup.
In his inauguration speech, Oligui vowed to hold "free, transparent and credible elections" to restore civilian rule, although he did not give a timeframe.
He also said he would shortly announce an inclusive transitional government drawing on figures from across the political spectrum.
Bongo, 64, took office in 2009 on the death of his father Omar, who ruled the central African state for more than 40 years, gaining a reputation as a kleptocrat.
He was re-elected by a wafer-thin margin in 2016, according to bitterly disputed official results, but two years later suffered a stroke that weakened his grip on power.
On August 30, soldiers led by Oligui, head of the elite Republic Guard, detained Bongo, his wife and son shortly after election overseers declared him victor in a presidential ballot four days earlier.
The oil-rich of Gabon state joins Mali, Guinea, Sudan, Burkina Faso and Niger among African countries that have undergone coups in the last three years.