Canadian David Veilleux of Europcar, the first-stage winner, kept the overall leader's jersey.
Boasson Hagen beat Australia's Michael Matthews and Belgium's Gianni Meersman to the line at the end of the 167km ride from Amberieu-en-Bugey.
The 26-year-old Boasson Hagen previously won a stage on the Dauphine in 2010 while he also won his home Tour of Norway last month.
Wednesday's fourth stage will be a 32.5km time-trial around the Parc des Oiseaux, near the town of Villars-les-Dombes.
Results from stage 3 of the Criterium du Dauphine (country/team):
1. Edvald Boasson Hagen (Norway / Team Sky) 4:03:32"
2. Michael Matthews (Australia / Orica) ST
3. Gianni Meersman (Belgium / Omega Pharma - Quick-Step)
4. Thor Hushovd (Norway / BMC Racing)
5. Elia Viviani (Italy / Cannondale)
6. Reinardt Janse Van Rensburg (South Africa / Argos)
7. Nacer Bouhanni (France / FDJ)
8. Paul Voss (Germany / NetApp)
9. Sylvain Chavanel (France / Omega Pharma - Quick-Step)
10. Francesco Gavazzi (Italy / Astana)
11. Geraint Thomas (Britain / Team Sky)
12. Florian Vachon (France / Bretagne)
13. Tony Gallopin (France / RadioShack)
14. Elia Favilli (Italy / Lampre)
15. Alejandro Valverde (Spain / Movistar)
16. Alexey Lutsenko (Kazakhstan / Astana)
17. Warren Barguil (France / Argos)
18. Alberto Contador (Spain / Saxo - Tinkoff)
19. Bram Tankink (Netherlands / Blanco)
20. Jakob Fuglsang (Denmark / Astana)
Overall Classification (country/team):
1. David Veilleux (Canada / Europcar) 12:00:22"
2. Gianni Meersman (Belgium / Omega Pharma - Quick-Step) +1:56"
3. Tony Gallopin (France / RadioShack) +1:57"
4. Alejandro Valverde (Spain / Movistar)
5. Warren Barguil (France / Argos)
6. Jakob Fuglsang (Denmark / Astana)
7. Geraint Thomas (Britain / Team Sky)
8. Angel Madrazo (Spain / Movistar)
9. Richie Porte (Australia / Team Sky)
10. Alberto Contador (Spain / Saxo - Tinkoff)
11. Chris Froome (Britain / Team Sky)
12. Dominik Nerz (Germany / BMC Racing)
13. Thomas Rohregger (Austria / RadioShack)
14. Peter Kennaugh (Britain / Team Sky)
15. Jurgen Van den Broeck (Belgium / Lotto)
16. Sylvain Chavanel (France / Omega Pharma - Quick-Step)
17. Samuel Sanchez (Spain / Euskaltel)
18. Rein Taaramaee (Estonia / Cofidis)
19. Christophe Le Mevel (France / Cofidis)
20. Daniel Navarro (Spain / Cofidis)