In wet conditions, the peloton gathered for a bunch sprint but the crash took out most of the pack leaving the Argos-Shimano rider to advance.
Mark Cavendish was unable to stay in touch and was six minutes off the pace.
Italy's Luca Paolini remains in the overall lead with Sir Bradley Wiggins still 34 seconds behind in sixth.
The Team Sky rider was one of those who appeared to have lost time as a host of riders slipped on the greasy surface, just a kilometre from the end of the 203km stage.
But organisers awarded the same time to the breakaway riders and the peloton as Degenkolb and a few others broke free.
That means the places of the top riders in the general classification stay the same, with Wiggins sixth overall and his team-mate Rigoberto Uran 17 seconds behind leader Paolini.
Unfortunately for Omega Pharma Quick-Step rider Cavendish, he was not part of the main group, and he finished disappointingly after struggling up a category four climb with 20km to go.
Stage five standings
1. John Degenkolb (Germany/Argos) 4:37:48"
2. Angel Vicioso (Spain/Katusha) same time
3. Paul Martens (Germany/Blanco)
4. Sergio Henao (Colombia/Team Sky)
5. Matteo Trentin (Italy/Omega Pharma Quick Step)
6. Jarlinson Pantano (Colombia/Colombia)
7. Daniel Oss (Italy/BMC Racing)
8. Jens Keukeleire (Belgium/Orica)
9. Grega Bole (Slovenia/Vacansoleil)
10. Tanel Kangert (Estonia/Astana)
General classification standings:
1. Luca Paolini (Italy / Katusha) 19:56:39"
2. Rigoberto Uran (Colombia / Team Sky) +17"
3. Benat Intxausti (Spain / Movistar) +26"
4. Vincenzo Nibali (Italy / Astana) +31"
5. Ryder Hesjedal (Canada / Garmin) +34"
6. Bradley Wiggins (Britain / Team Sky)
7. Giampaolo Caruso (Italy / Katusha) +36"
8. Sergio Henao (Colombia / Team Sky) +37"
9. Mauro Santambrogio (Italy / Vini Fantini) +39"
10. Cadel Evans (Australia / BMC Racing) +42"
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