More than 30 riders were injured in the pileup, which occurred 52 kilometres from the finish line on the stage in Belgium.
It occurred when FDJ rider William Bonnet went down and others just careered into the back of him while travelling at an average speed of 42.03 kilometres an hour, according to Tour de France organizers.
Cancellera, 35, was among several riders injured in the accident, which forced organizers to temporarily stop the race as doctors attended to the wounded.
The Bern native, who has won eight stages of the Tour de France in his career, got back on his bike but finished well back of the leaders and afterwards sought treatment for bone fractures.
“Just left the hospital with a huge disappointment,” Cancellera tweeted.
This year’s Tour de France “is over broke some bones on my back again as in spring”, he said referring to back injuries he suffered at the E3 Harelbeke race in Belgium in March.
For Cancellera, who was won the Tour of Flanders and Paris-Roubaix races three times, the fall was a tough blow, as it was for the other competitors thrown off course by the spectacular collision.
UK rider Chris Froome, winner of the 2013 Tour de France, took over the yellow jersey.
Check out the accident in the video below from Le Tour de France:
La minute maillot jaune LCL - Étape 3 (Anvers... par tourdefrance