Degenkolb, of Giant-Shimano, edged the bunch sprint to beat Arnaud Demare into second, with in-form defending champion Peter Sagan third.
A late three-man breakaway of Stijn Devolder, Andrey Amador and Silvan Dillier was caught with just over a kilometre left of the 233km day race, with Degenkolb showing his delight in snatching the win.
There were several crashes along the way, with Ian Stannard taken to hospital after ending up in a ditch. His GB and Team Sky colleague Geraint Thomas also fell, but remounted and finished the race.
1. John Degenkolb (Ger) Giant-Shimano, 5:34:37
2. Arnaud Demare (Fra) FDJ, same time
3. Peter Sagan (Svk) Cannondale
4. Sep Vanmarcke (Bel) Belkin
5. Tom Boonen (Bel) OmegaPharma-QuickStep
6. Tom van Asbroeck (Bel) Topsport Vlaanderen-Baloise
7. Alexey Tsatevich (Rus) Katusha
8. Yauheni Hutarovich (Blr) Ag2r-La Mondiale
9. Thor Hushivd (Nor) BMC
10. Jurgen Roelandts (Bel) Lotto Belisol
- Sports & Recreation
- Peter Sagan
- Arnaud Demare
- Andrey Amador
- Silvan Dillier
- Stijn Devolder