The Spanish Euskaltel-Euskadi rider briefly lost consciousness following the incident between France's Belfort and the Swiss town of Porrentruy.
The rider lay in the road receiving medical attention for several minutes and was then taken away on a stretcher.
Race organisers said in a statement that hospital scans had shown the hand fracture and trauma to the left shoulder but that he had not fractured his collarbone as had been feared.
The road race at the London Games takes place on July 28.
This year's Tour has been marred by a series of pileups which have resulted in an array of broken bones.