Off the back of the peloton following a second mechanical, Schär was shown tossing a bidon on the ground to the side of the track towards a group of spectators.
After making his way back into the peloton, he was told by the race commissaires of his disqualification and was instructed to stop riding.
The sanctions are part of updated UCI rules in regards to littering, with the governing body announcing earlier this year riders could be fined, docked ranking points and penalised time if they throw objects such as bidons and waste in a careless or dangerous manner or outside of new litter zones.
The new rules mean riders can only drop litter at specific points during races, or hand it to team officials directly.
Schär was not the only disqualification from this year's Tour of Flanders, with Otto Vergaerde (Alpecin-Fenix) and Yevgeniy Fedorov (Astana) kicked out following an altercation early in the race in which elbows and angry words were exchanged.