Froome, who has a 12-second advantage over Alberto Contador, came down on a descent out of the town of Chavanod.
Despite nursing several visible cuts, the Sky rider quickly made it back into the peloton.
By then, the day’s break had an unassailable advantage. Bakelants was part of a 16-man group that formed after an hour of racing, but it was an attack from Pim Lightart (Lotto-Belisol) with around 25 kilometres remaining that decided the result.
Lightart jumped from the leading group, and was followed by Astana’s Lieuwe Westra. Bakelants eventually bridged across, before Lighthart was dropped on one of a handful of undulations that lined the route approaching the finish.
Westra started his sprint with 225 metres remaining having moved into the perfect line to tackle a sweeping final bend. However, he nearly pushed the onrushing Bakelants into the barriers to his right, and seemingly sensing the likelihood that this move would get him relegated should he win the stage, appeared to ease off in the final 25 metres to allow Bakelants to seal the victory.
Froome led home the peloton, surrounded by team-mates Richie Porte, Mikel Nieve and David Lopez, nearly four minutes later.
Critérium du Dauphiné 2014, stage six: Grenoble – Posiy 168km
1. Jan Bakelants (Bel) Omega Pharma-Quick Step in 4-07-20
2. Lieuwe Westra (Ned) Astana
3. Zdenek Stybar (Cze) Omega Pharma-Quick Step Cycling Team at 0-24
4. Pim Ligthart (Ned) Lotto-Belisol
5. Jens Keukeleire (Bel) Orica GreenEdge
6. Jens Voigt (Ger) Trek Factory Racing
7. Maciej Bodnar (Pol) Cannondale
8. Bram Tankink (Ned) Belkin
9. Valerio Conti (Ita) Lampre-Merida
10. Julien Simon (Fra) Cofidis all at st.
General classification after stage six
1. Christopher Froome (GBr) Team Sky in 23-12-15
2. Alberto Contador Velasco (Spa) Tinkoff-Saxo at 0-12
3. Wilco Kelderman (Ned) Belkin at st.
4. Andrew Talansky (USA) Garmin-Sharp at 0-33
5. Jurgen Van Den Broeck (Bel) Lotto-Belisol at 0-35
6. Vincenzo Nibali (Ita) Astana at 0-50
7. Haimar Zubeldia Agirre (Spa) Trek Factory Racing at 1-22
8. Jakob Fuglsang (Den) Astana Pro Team at st.
9. Adam Yates (GBr) Orica GreenEdge at 1-24
10. Tanel Kangert (Est) Astana at 1-35