The 20-year-old sprinter, who won the Olympic omnium silver medal at London 2012, recorded his first professional victory on the road in a bunch gallop at the end of the 157km stage from Nimes.
He beat stage one winner Michael Van Staeyen (Topsport Vlaanderen-Baloise) to the line although the Belgian retains the overall lead.
Baptiste Planckaert (Crelan-Euphony), Stefan Van Dijk (Accent Jobs) and Jonas Van Genechten (Lotto-Belisol) completed the top five.
Thomas Vaubourzeix (La Pomme Marseille), Alphonse Vermote (An Post – Chainreaction) and Jimmy Engoulvent (Sojasun) escaped early and had a lead of just over six minutes at the 70km mark.
They crossed the two king of the mountains climbs still well ahead. Their lead was at 3:50 with 67km to go but that was gradually whittled down to two minutes with 30km remaining before the sprinters' teams completed a successful chase with 13km remaining.
"We were pulling hard on the front of the peloton going into the final kilometre," said Europcar directeur sportif Dominique Arnould.
"Bryan was in the wheel of Seb (Chavanel), who lead him out brilliantly. Bryan then had to seal the deal in the final 200m.
"To do this in only his second race as a professional is incredible.
"It's going to take a huge amount of weight off his shoulders too. The whole world was expecting great things from Bryan. The team put its confidence in him, and he proved just what he's capable of. The goal has been accomplished."
Stage three of the early-season five-day race held annually in Southern France sees the riders travel 152km, beginning and finishing in Besseges.