Spaniard Contador, one of the pre-race favourites, was among the riders caught up in a crash with four kilometres left and he crossed the line with the left side of his jersey torn up and his face a mask of pain.
"He is all right but it is after the night that we will see how he has recuperated from the crash. There is no fracture," Contador's sports director at Team Saxo-Tinkoff, Philippe Mauduit, told reporters.
Contador told reporters: "It hurts. We put ice on it. The Tour is the Tour, you never know what can happen."
Slovakian prodigy Peter Sagan, who won the green jersey for the points classification last year, also crashed as the peloton got jittery when they heard the finish line had been moved to the three-kilometre line.
Double time-trial world champion Tony Martin of Germany crashed heavily, too, and suffered a lung contusion, concussion, and a deep wound on his left elbow. He was carried on a stretcher into an ambulance from his team bus.
Team Sky will have their full complement of nine riders at the start of Sunday's second stage, a 156km hilly ride to Ajaccio, after Geraint Thomas and Ian Stannard were cleared to continue. The duo also crashed heavily.
Pre-stage favourite Mark Cavendish of Britain was held up behind the crash that took down dozen of riders and could not contest the final sprint.
"I count myself lucky," the British champion said.
The Orica-GreenEdge team bus was eventually moved away before the peloton's arrival.
Organisers said that all riders would be credited with the same time because of the incidents.
"Eight kilometres from the finish I informed the teams that the line was being moved to three kilometers from the finish," race director Jean-Francois Pecheux told reporters.
"Then I was informed that eventually the bus was moved and I told the teams that the original finish line was maintained, which disturbed the peloton."
Fabrizio Guidi, the other sports director at Team Saxo-Tinkoff, said: "It was an insanely chaotic stage and it's really a shame for everyone that the stage was opened in this chaos. We were confused to say the least in the car behind the field.
"First we were told that the finish line was moved because of a bus blocking the road. We passed the information on to the riders, who then did the sprint.
"The moment later, the finish line was moved back to its original spot and then in all the confusion the big crash happened."
There were also early nerves for overwhelming favourite Chris Froome of Britain, who suffered a minor crash in the neutral zone before the start. He escaped unhurt.
"I managed to get through the rest of the day unscathed and if that is the only crash I have this Tour I will take that", Froome said.
"I don't think any of us expected it was going to be plain sailing today, but there were some pretty brutal crashes in the final there.
"Again, it is just another reminder that this Tour is about so much more than having the form and being here. It is about staying out of trouble and looking after ourselves in the peloton at the same time."