Bouhanni (Cofidis) finished the 173km stage from Le Bourget-du-Lac to Villars-les-Dombes ahead of Samuel Dumoulin (AG2R) and Sacha Modolo (Lampre-Merida) to give himself a big boost of confidence ahead of July's Tour de France.
"I'm in the build up for the Tour de France which is my main goal of the year," Bouhanni said. The Dauphiné and the French championship are part of a very important period for me.
Arnaud Courteille (FDJ), Perrig Quemeneur (Europcar) and Daniel Teklehaimanot (MTN-Qhubeka) crafted an early escape and built a maximum lead of 6 minutes and 50 seconds before they got reined in with 3.5km to go after a 170km long breakaway.
The stage finale was marred by a crash involving Wilco Kelderman (LottoNL-Jumbo) before Bouhanni made the most of the flat finish to secure the victory.
"There was a head wind at the end today so I needed to stay protected by my team-mates," Bouhanni said. "I was well positioned in Geoffrey Soupe's wheel, I didn't care about my adversaries. I let him put himself behind (Edvald) Boasson Hagen, then Modolo, and I managed to accelerate with 200m to go.
"Yesterday I was disappointed but there was a very nice winner with Peter Kennaugh's coup. This is my fourth win this year and my first one at World Tour level. I'm on the right track but I won't stop here.
"After tomorrow at Sisteron (a team time trial) there'll be another possibility for a bunch sprint finish. If there's an opportunity to get a second stage win, I won't let it go."
Kennaugh, who rides for the Sky team, led by former Tour de France champion Chris Froome, maintains a two second lead in the overall standings over Modolo and Bouhanni.
Defending Tour de France champion Vincenzo Nibali (Astana) and the 2013 winner Froome, two of the main contenders for the overall victory, finished in the main bunch and are well positioned behind Kennaugh.
Stage 3 features a team time-trial over 24.5km between Roanne and Montagny with the race set to finish on Sunday.
Stage 2: 173km, Le Bourget-du-Lac - Villars-les-Dombes
1 Nacer Bouhanni (FRA) Cofidis, 4hr 23min 46sec
2 Samuel Dumoulin (FRA) AG2R
3 Sacha Modolo (ITA) Lampre-Merida
4 Edvald Boasson Hagen (NOR) MTN-Qhubeka
5 Aleksei Tsatevich (RUS) Katusha
6 Jonas Vangenechten (BEL) IAM
7 Jens Keukeleire (BEL) Orica-GreenEDGE
8 Ramunas Navardauskas (LTU) Cannondale-Garmin
9 Yannick Martinez (FRA) Europcar
10 Luka Mezgec (SLO) Giant-Alpecin
1 Peter Kennaugh (GBR) Sky 7hr 30min 27sec
2 Sacha Modolo (ITA) Lampre-Merida 0:00:02
3 Nacer Bouhanni (FRA) Cofidis
4 Samuel Dumoulin (FRA) AG2R 0:00:06
5 Edvald Boasson Hagen (NOR) MTN-Qhubeka 0:00:08
6 Tiesj Benoot (BEL) Lotto-Soudal 0:00:12
7 Yannick Martinez (FRA) Europcar
8 Jay McCarthy (AUA) Tinkoff-Saxo
9 Ramunas Navardauskas (LTA) Cannondale-Garmin
10 Julian Alaphilippe (FRA) Etixx-QuickStep