The Spaniard, blood also dripping from his knee, spent several minutes being treated by race doctors during the 10th Stage.
His Tinkoff-Saxo manager Bjarne Riis told reporters that Contador, who was hoping to win his third Tour after victories in 2007 and 2009, suffered a broken shinbone and would undergo surgery.
The organisers' medical statement confirmed the nature of the injury, adding that he also suffered an elbow problem.
There was no TV footage of the accident, but Vincenzo Nibali, on his way to a solo victory in Monday's stage to reclaim the yellow jersey, witnessed it first hand.
"It happened in a descent, the asphalt was not in good condition. He was behind me but then passed me and three seconds later he fell off in front of me. It was spectacular, we were around 60 kph," the Italian champion said.
"I was just behind and for a moment I thought my Tour could be over too."
After being treated by doctors, Contador got back on his bike but after climbing the category-one Col du Platzerwasel with the help of his Tinkoff-Saxo team mates, he dismounted and stepped into his team car.
The peloton, led by his main rival Nibali's Astana team, was already some four minutes ahead.
"Alberto crashed badly. His right knee is seriously injured. The crash has been violent. I have his shoe with me, it's completely destroyed," said Contador's sports director Philippe Mauduit.
"According to some rumours, his bike has been broken but that's not the case. A bike fell from our racks after we fixed Nicolas Roche's bike.
"Before pulling out, he told us he was in awful pain and he couldn't go any further on his bike. It's a pity because everything had gone well since the beginning of the Tour. We had a plan and today's race was unfolding exactly as we wanted," added Mauduit.
"In a fraction of a second, it all fell apart, so we're immensely sad."
Contador was the second top favourite to pull out of this year's race after reigning champion Chris Froome of Britain crashed during the fifth stage.
Froome sent his rival a message of support on Twitter, recognising Contador's exit was a "big loss for the TDF today."
"Recover well @albertocontador and I hope to see you at the Vuelta," added the Briton, referring to Contador's home race in Spain.
Tinkoff-Saxo issued a statement confirming Contador's withdrawal due to injury.
"After receiving medical care and a new bike, Alberto was determined to get back on the bike and quickly continued in an attempt to close the gap to the peloton," the team said.
"Tinkoff-Saxo’s attempt to bring Alberto back in the peloton was made difficult by the mountainous terrain and the high speed up front."
Contador had started the day ninth overall, 4:08 behind France's Tony Gallopin and 2:34 behind Nibali.
(Reporting by Julien Pretot; Editing by Alan Baldwin and Tony Goodson)
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