The Welshman hit the deck on the descent of the Col de la Biche with just over 100 kilometres left to race. Thomas started the stage sitting second overall on GC, 12 seconds down on teammate Chris Froome.
Thomas won the opening stage of the race in Germany, and wore the maillot jaune until stage 5, when he handed it over to Froome on the first summit finish of this year's race. He crashed out of the Giro d'Italia in May after hitting a poorly parked police motorbike and made his racing comeback at the Tour.
Thomas has crashed several times during the Tour de France, and fell as recently as stage 8 when he overcooked a corner and went over the bars.
Thomas was taken straight to hospital for examinations and Team Sky later confirmed he had suffered a fracture to his right collarbone.
"Geraint has broken his collarbone, which is just devastating for him really," team principal Dave Brailsford told Eurosport at the finish in Chambery.
"He had the crash at the Giro, then the rollercoaster of coming here and getting yellow, then the collarbone today. We can say 'dust down and bounce back' and everything, but the reality is that that's tough. We'll put our arm around him and help him back."