A panel chaired by five-times Tour de France champion Bernard Hinault voted for the 21-year-old prospect.
Berhane, who is yet to make his professional debut with Europcar, pipped South Africa's Reinhardt Janse Van Rensburg and Morocco's Adil Jelloul to the award.
"The trophy created this year by the Gabonese (Tropicale Amassa Bongo race) organisers rewards the African cyclist who made the greatest impact during the season especially in events on the African continent," read a statement.
Berhane picked up three titles at the African championships in November and won the Tour of Algeria and the Tour du Chablais, a French amateur classic.
"Natnael Berhane left his mark on people for his consistency," the statement added.
1. Natnael Berhane (ERY) 72 points
2. Reinhardt Janse Van Rensburg (RSA) 41
3. Adil Jelloul (MAR) 39
4. Tarik Chaoufi (MAR) 37
5. Meron Russom (ERY) 18