The 22-year-old Frenchman beat overall leader Andrea Palini of Lampre-Merida to the line at the end of the 109km stage which travelled through tropical forest from Oyem to Mitzic.
Lotto-Belisol duo Vicente Reynes and Gaetan Bille followed them home.
The stage was animated by a five-man breakaway which included last year's runner-up Meron Russom and saw the Eritrean, riding for MTN-Qhubeka, in the virtual race lead.
The quintet led by 1:40 with 12km to go but the blue and fuchsia jerseys of stage two winner Palini reeled them in to set up a bunch gallop to the line.
The eighth edition of Africa's only race rated 2.1 by the UCI sees nine African national teams join UCI ProTeams Lampre-Merida and Lotto-Belisol plus Europcar, Cofidis, Groupement Sportif Oil and MTN-Qhubeka in the seven-day race.
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