The German will require surgery after displacing his collarbone 8.2 kilometres from the finish in Wevelgem.
The Lotto-Belisol rider was the pre-race favourite in Belgium and the team have been left rocked by the news.
"This is a big blow for Andre and the whole team," admitted Lotto manager Marc Sergeant.
"He was our plan for many events – like the Tour of Flanders and Paris Roubaix."
John Degenkolb won his biggest-ever Classic by sprinting to victory at the Gent-Wevelgem.
Degenkolb, of Giant-Shimano, edged the bunch sprint to beat Arnaud Demare into second, with in-form defending champion Peter Sagan third.
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