With around 60 km to go to the finish line, Philipsen hit the road hard following contact with Bryan Coquard during an intermediate sprint.
The Alpecin-Deceuninck rider had his jersey ripped in several places and suffered bloody scrapes. He was attended to by the race doctor shortly afterwards.
"Displaced fracture of the right collarbone, surgery will definitely be required. At least one broken rib, possibly two. He will be as soon as possible transferred to the hospital in Herentals, where he will undergo surgery," Alpecin-Deceuninck revealed.
Philipsen, who was also wearing the green jersey, ends his Tour on a sour note despite having won the opening stage on Saturday. The race continues around France and finishes on July 27th.
"It's clear that the other two riders collided and as a result Jasper was hit and crashed badly. There's a reason for it but we're not talking about who's to blame, it's a case of bad luck and an incident in the race," Philipsen's manager Philip Roodhooft said.
"But obviously the circumstances for us as a team and for Jasper individually are terrible," he said. "It's a blow to the mental health of the whole team and it's the worst thing for Jasper. But it goes on."
Coquard was visibly emotional in the aftermath of the race.
"I was clearly off balance and lost the pedal. I'd like to apologise to Philipsen and Alpecin, even if it wasn't deliberate. Even though I'm not a bad lad, it wasn't pleasant," he said.
Philipsen was not alone in hitting the tarmac on the flat stretch between Valenciennes and Dunkirk, as multiple separate crashes occurred in the final stretch before the finish.
A crash three km from the finish line brought down several riders, including Remco Evenepoel. Another pile-up followed at the final turn, with Cees Bol and Alexis Renard among those affected.
Belgium's Tim Merlier ended up winning the stage in a sprint finish ahead of Italy's Jonathan Milan.