German powerhouse Kittel of Argos-Shimano took the victory in an uphill finish at Cerilly at the end of a 200km stage from Vimory.
Kittel, who was in the second group on Monday and unable to contest the sprint, was a clear winner from Elia Viviani (Cannondale) who inherits the yellow jersey.
The Italian, who also took the final intermediate sprint of the day, now leads by seven seconds on GC from Sylvain Chavanel (Omega Pharma-Quick Step) after French champion Bouhanni was forced to quit the race after crashing on a left hand corner with 55km to go.
Early reports suggested that the FDJ rider was bruised but had suffered no fractures or broken bones.
Latvia's Gatis Smukulis (Katusha), Belgium's Kris Boeckmans (Vacansoleil-DCM) and Dane Mads Christensen (Saxo-Tinkoff) escaped almost immediately after the start but they were back in the peloton at the 55km mark.
The average speed for the second hour of the race was just 26.7kph with reports that riders were riding slowly in protest at the stage distance.
After 70km, Mikel Astarloza (Euskaltel), Maxime Bouet (AG2R), Thomas de Gendt (Vacansoleil-DCM) and Romain Feillu (Vacansoleil-DCM) went away and swiftly built up a lead over four minutes.
But they were caught with 45km remaining to set up the inevitable bunch sprint. The ORICA-GreenEDGE train hit the front in the final stages but the 4% uphill finish caused a messy sprint and their man Leigh Howard had to settle for third.