Ndong-Sima, served as prime minister under Bongo from 2012 to 2014 before becoming a critic and eventually challenging him in elections in 2016 and 2023.
His appointment was made in a decree by the new strongman, General Brice Nguema, who was sworn in as interim president on Monday after the coup.
In his inauguration speech, Nguema had vowed to hold free, transparent and credible elections to restore civilian rule.
He also said he would shortly announce an inclusive transitional government drawing on figures from across the political spectrum.
