The Spaniard, victorious in the past two grands prix, crashed early on when he fell foul of a combination of white lines and standing water heading into the sixth-gear Turn 13.
Lorenzo was flung over his handlebars at an estimated150mph and appeared to land on his left shoulder, which he then seemed to be nursing as he walked to the ambulance.
Organisers confirmed shortly after the chequered flag that he had suffered a collarbone fracture.
He will now miss Saturday's race at the Dutch circuit, instead staying in hospital for observation before flying to Barcelona for surgery on Friday.
Lorenzo is currently seven points behind MotoGP championship leader Dani Pedrosa in the standings.
The 26-year-old did not finish last year's Dutch Grand Prix after being wiped out by Alvaro Bautista at Turn 1, but went on to clinch a second MotoGP crown, 18 points ahead of current points leader Dani Pedrosa.