Belgian Dockx, who also won Wednesday's third stage, claimed the seventh ahead of Tsgabu Grmay (MTN-Qhubeka) and Lotto Belisol team-mate Frederique Robert.
But, having taken the leader's yellow jersey after an emphatic win from a break in the penultimate stage, Gene secured the overall.
Winning the Tropicale Amissa Bongo is becoming something of a habit for Jean-Rene Bernaudeau's riders. After three successive overall wins for Frenchman Anthony Charteau it was the turn of his compatriot to take the spoils – and notch his first ever overall win in a stage race.
The 31-year-old sprinter showed promising form all week with a string of top 10 finishes in the opening five stages. But it was his winning break in Saturday's 147km stage from Lambarene to Kango that saw Gene shoot to the top of the standings.
Victory in Kango was Gene's sixth scalp in the Tropicale Amissa Bongo and came thanks to some expert support from team-mates Natnael Berhane and Christophe Kern, both of whom were also part of the decisive break.
Outsprinting Moroccan Soufiane Haddi and Belgium's Gaetan Bille (Lotto-Belisol), Gene took the overall lead from the long-time leader Andrea Palini of Italy (Lampre-Merida).
Knowing that a strong finish within the peloton in Sunday's final stage would be enough, Gene finished safely to conserve his eight-second lead over Moroccan Soufiane Haddi in the GC. Belgian Gaetan Bille completed the final podium, 14 seconds behind the race winner .
"I am immensely happy to have won because Gabon is a country I adore," said Gene. "The climate and the atmosphere reminds me of my native Guadeloupe and that was a huge factor in my success here in the Tropicale."