World champion Peter Sagan was disqualified from the Tour by the race jury for causing the crash, which sent Cavendish into the barriers 120 metres before the finish line.
Cavendish had spent three months battling back from the Epstein-Barr virus in order to make the start line of the Tour in Dusseldorf, and his early exit will come as a bitter blow.
“I’m obviously massively disappointed to get this news about the fracture,” Cavendish said. “The team was incredible today.
“They executed to perfection what we wanted to do this morning. I feel I was in a good position to win and to lose that and even having to leave the Tour, a race I have built my whole career around, is really sad.”
As news broke of Cavendish’s departure, Sagan’s Bora-Hansgrohe team announced they had officially protested the Slovakian’s expulsion.
The German squad said Sagan “rejected to have caused, or in any way intended to cause the crash of Mark Cavendish”, adding the 27-year-old could not see Cavendish as the Manxman tried to come up on his right-hand side.
Sagan, who was initially penalised 30 seconds for the incident before the race jury reviewed the footage, had finished second to Arnaud Demare of FDJ in the sprint prior to his disqualification.
“In the sprint I didn’t know that Mark Cavendish was behind me,” Sagan said.
“He was coming from the right side, and I was trying to go on (Alexander) Kristoff’s wheel. Mark was coming really fast from the back and I just didn’t have time to react and to go left.
“He came into me and he went into the fence. When I was told after the finish that Mark had crashed, I went straight away to find out how he was doing.
“We are friends and colleagues in the peloton and crashes like that are never nice. I hope Mark recovers soon.”
There had initially been optimism regarding Cavendish’s status as tests at a local hospital found no signs of a break.
But after he travelled to Nancy for further scans the picture changed.
“Mark suffered a fracture to the right scapula,” Team Dimension Data doctor Adrian Rotunno said. “Fortunately no surgery is required at this stage, and most importantly there is no nerve damage.
“He’s been withdrawn from the race for obvious medical reasons, and we’ll continue monitoring him over the coming days.”
The news means the 32-year-old’s hopes of adding to his 30 career Tour stage wins and closing in on Eddy Merckx’s all-time record of 34 are over for another year.
Sagan came into the Tour as an overwhelming favourite to win the points leaders’ green jersey for a record-equalling sixth straight time, having won it every year since his Tour debut in 2012.
But the race jury judged his actions to be dangerous and exercised their power to kick him out of the race.
“We have decided to disqualify Peter Sagan from Tour de France 2017 as he endangered some of his colleagues seriously in the final metres of the sprint which happened in Vittel,” said race jury president Philippe Marien.
“We applied article 12.104, irregular sprints, in which case commissaires are allowed to enforce a judgement to disqualify a rider and amend a fine.”
The incident happened moments after another crash had sent Team Sky’s Geraint Thomas to the deck in the race leaders’ yellow jersey.
Thomas was fine to continue, losing no time as the incidents occurred inside the final three kilometres, while Chris Froome managed to skirt around it.
“I’m all right,” Thomas said. “It was just a crash in front of me and I had nowhere to go.
“Luckily I took off most of the speed. I think Froomey managed to get round it and he’s okay.”
Thomas continues to lead from Froome by 12 seconds, with Michael Matthews of Team Sunweb on the same time in third place overall going into Wednesday’s stage to La Planche des Belles Filles, where the fight for yellow is expected to ignite.