The Welshman went down in a fall at the front of the bunch around 144km from the finish of stage three from Lorient to Pontivy.
Ineos Grenadiers have confirmed that Thomas dislocated his shoulder in the race, which was put back in place on scene by the race doctor.
Thomas then went for an ultrasound scan after the finish, with results due to be confirmed this evening.
The crashed happened near the front of the peloton as Thomas's Ineos team went over a speed bump, with the Welshman falling hard.
After laying on the floor and looking to be in some serious discomfort, video from the moments after the fall showed a race doctor appearing to pop Thomas's shoulder back into place.
Ineos Grenadiers leader Thomas was able to remount the bike and continue on, re-joining the peloton after a 20km chase with the assistance of his team-mates.
Jumbo-Visma rider Robert Gesink went down in the same crash and was forced to abandon the race.
While Thomas was initially able to rejoin the peloton and initially avoid any time losses, the finale was marred by further crashes, with Primož Roglič (Jumbo-Visma) falling hard 10km from the finish and losing time.
Those crashes in the final caused a number of splits in the bunch, with 17 riders making it to the finish together, as Tim Merlier (Alpecin-Fenix) won the stage.
Meanwhile, Thomas finished in the third group on the road in 48th place, 26 seconds behind the stage winner.
Thomas, winner of the 2018 Tour de France, lost time to his team-mate Richard Carapaz who finished in the front group along with general classification rival Julian Alaphilippe (Deceuninck - Quick-Step).
After stage three, Thomas has moved up two places overall into 18th place, 1-07 behind current yellow jersey holder Mathieu van der Poel (Alpecin-Fenix).
Alaphilippe is second overall eight seconds behind Van der Poel, while Carapaz jumps into third, 31 seconds off the race lead.
Tadej Pogačar (UAE Team Emirates) finish in the same group as Thomas and is now sixth overall, 39 seconds down.
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