The Welsh rider is believed to have dislocated his shoulder after he went down heavily 37 kilometres into the 187km route between Lorient and Pontivy.
The INEOS co-leader become caught up as riders at the front of the peloton touched wheels, with Jumbo Visma riders Tony Martin and Robert Gesink also going to ground.
Thomas was seen prone in the centre of the road after the crash and appeared in extreme pain as medics put his shoulder back in place.
While Gesink was forced to retire from the race as a result of his injuries, Thomas powered on after gingerly retaking his saddle to resume racing.
INEOS teammates Luke Rowe, Jonathan Castroviejo and Dylan Van Baarle all dropped off to help Thomas make up the three-minute gap to the peloton, rejoining the main group with 125km left in the stage.
Thomas still appeared in discomfort and had ripped his shorts with slight grazing visible.
A long afternoon lay in store for Thomas, who dropped back to the medical car for some in-the-saddle treatment.
Thomas was 41 seconds off the pace in the general classification at the start of the stage.
