Initially it was suspected that Boonen had fractured his collarbone, but a medical examination revealed an acromioclavicular (AC) joint dislocation which requires a period of recovery from three to six weeks.
"An AC-joint dislocation, as we've already seen with other riders of the team with the same kind of injury, requires an extended time of recovery due to the nature of the injury," Etixx-QuickStep team doctor Yvan van Mol said in a statement
"Unfortunately, because of the injury and the time it takes to recover, Boonen will not be able to participate in the Northern Classics. Tomorrow Tom will undergo further examination in Belgium to diagnose the grade of the dislocation and determine if surgery is necessary based on the grade."
Boonen collided with a Cannondale-Garmin rider with 16 kilometres to race in the 192-kilometre stage to Contres. He sat on the ground and held his left arm while his Etixx team and the race doctor examined him. Eventually he took off his helmet and abandoned the stage.
The crash comes at the worst time for the 34-year-old with only two weeks to go until the big Classics begin.
"We'll provide official information from the team about [Boonen] as soon as we can," Etixx wrote on Twitter just after the incident happened. "We appreciate your patience and concern."
2005 World Champion Boonen is one of the most successful Classics cyclists currently racing. His palmarès includes three wins in the Tour of Flanders and four in Paris-Roubaix.
He demonstrated his form in 2015 by placing third in the Omloop Het Nieuwsblad behind Ian Stannard (Sky). However, with a typical recovery period of up to six weeks, he will be unable to use his strength in the Classics.
In 2012, Boonen won both the Tour of Flanders and Paris-Roubaix. In 2013, he crashed in Ghent-Wevelgem and early into Flanders, which forced him to abandon and miss Roubaix.
This year's Paris-Roubaix, the last of the Classics that suits Boonen, takes place on April 12.
Alexander Kristoff (Katusha) won today's Paris-Nice stage, but Boonen's team-mate and World Champion Michal Kwiatkowski continues to wear the yellow leader's jersey after his win in yesterday's prologue.
Thank you for reading 5 articles this month* Join now for unlimited access
Enjoy your first month for just £1 / $1 / €1
*Read 5 free articles per month without a subscription
Join now for unlimited access
Try first month for just £1 / $1 / €1