The 29-year-old Briton slammed into the tarmac within sight of the finish and, although he limped over the line, a medical bulletin said he had dislocated his right shoulder, putting his further participation in the race in doubt.
His Omega Pharma-Quick Step team said in a statement that a decision on whether he could continue would be made on Sunday morning before the start of the second stage.
The Manx Missile was perfectly placed to seize the yellow jersey for the first time in his illustrious career after his team led him out along Harrogate’s sunlit Parliament Street.
With huge crowds cheering him on, he tangled with Australia’s Simon Gerrans and the two riders crashed spectacularly to the ground. Cavendish winced in pain and clutched his right shoulder.
After finally crossing the line three minutes 37 seconds after Kittel, he was whisked straight to the team bus and later taken to hospital for scans.
The Tour’s medical service described the injury as a right shoulder trauma and a “dislocation between the collarbone and the acromion”.
Kittel, who also won the first stage last year as well as three others, avoided the mayhem to snatch victory, easily outsprinting Slovakian Peter Sagan and Lithuanian Ramunas Navardauskas.
Defending champion Chris Froome was sixth.
Kittel was presented with the race leader’s yellow jersey by the Duchess of Cambridge who also cut the tape at the ceremonial start at the 18th Century Harewood House.
“It was so hard,” said the Giant Shimano rider who last year beat Cavendish 4-2 in Tour stage wins.
“The hill in the last kilometre made it very difficult to win. There were so many people that we rode the finale like in a tunnel with a terrible noise,” added Kittel.
“It’s unbelievable I’ve won stage one again. I had good legs today and my guys did an excellent job. I feel sorry for Mark Cavendish and I wish him all the best.”
Cavendish, aiming for a 26th Tour de France stage victory, seemed too eager to succeed in the closing stages and, using his shoulders for extra leverage, appeared to sway towards Gerrans, bringing both of them down.
“I’m gutted about the crash today,” Cavendish said.
“It was my fault. I’ll personally apologise to Simon Gerrans as soon as I get the chance. In reality, I tried to find a gap that wasn’t really there.
“I wanted to win today, I felt really strong and was in a great position to contest the sprint thanks to the unbelievable efforts of my team. Sorry to all the fans that came out to support – it was truly incredible.”
His team manager Patrick Lefevere could not say whether Cavendish’s race was over.
“Mark had lived this sprint in his mind at least 100 times before,” he told reporters outside the team bus as media crews swarmed around for news. “He was so focused, he wanted to win so badly.
“He told me Simon Gerrans slowed down and he really wanted to get out and he pushed and Gerrans pushed back. And that’s how he crashed.”
Orica GreenEdge sports director Matt White said Gerrans was in contention for victory until the crash.
“Cav was very hungry to win this stage wasn’t he? It was a once in a lifetime thing for him to have the yellow jersey. I can’t speculate on what he was feeling,” said White.
“Simon was in a very good position to launch a sprint for the win.”
A sensational 190.5-km opening stage from Leeds took the 198 riders across the spectacular Yorkshire Dales and included three categorised climbs – all of which attracted massive crowds as the Tour returned to Britain seven years after London staged the Grand Depart.
Jens Voigt made it a great day for Germany as the 42-year-old veteran, part of a three-man breakaway group including Frenchmen Nicolas Edet and Benoit Jarrier, went off alone after the intermediate sprint.
As he powered up the Cote de Buttertubs, in what is his record 17th and last Tour, massed ranks of fans gave the impression of a mountain-top finish in the Alps.
Voigt was eventually reeled in but his reward was the polka dot jersey for the mountain classification.
The stage was no walk in the park and several riders, including Spain’s Joaquim Rodriguez and top French hope Thibaut Pinot, were caught off guard when the peloton split.
They made it back to the bunch who were slowed by the big crowds on some narrow roads.
Sunday’s second stage is a treacherous 201-km trek from York to Sheffield.
(Editing by Julien Pretot and Clare Lovell)