In the final descent to Chambery, Porte missed a downhill bend, cartwheeling across the road and bowling over another rider, Dan Martin, before hitting a rocky bank.
Live broadcasts on French television showed Porte lying motionless in the road being treated by a medic, before being loaded into an ambulance wearing a neck brace.
“He was conscious, it’s reassuring, he is being transferred to the hospital,” race doctor Florence Pommery said.
Porte was in a group of seven riders, including race leader Chris Froome, who were descending from the last of seven climbs during Sunday’s mountain stage.
The Australian had been fifth overall.