Ndong Sima, a 68-year-old Paris-educated economist, served as prime minister under Bongo from 2012 to 2014 before becoming a critic and competing against him in the 2016 and 2023 presidential campaigns.
His appointment, announced on state TV, was made in a decree by the new strongman, General Brice Oligui Nguema, who was sworn in as interim president on Monday.
In his inauguration speech, Oligui vowed to hold "free, transparent and credible elections" to restore civilian rule, but did not give a timeframe.
He also said he would soon announce a transitional government that drew on figures from across the political spectrum.
The country would also draw up a new constitution, drafted with representatives from all the key groups, which would be "more respectful of democracy and human rights" and submitted to a referendum, Oligui said.