The home favourite fell heavily after losing control of his Yamaha at high speed in turn 13 in cold and wet conditions and missed the afternoon qualifying session in which Alvaro Bautista claimed a shock pole.
Crutchlow was taken to hospital for further examination of his injury, with the rider in significant discomfort, but that revealed a sprained ankle rather than a fracture, meaning he could still start Sunday's race, albeit from the back of the grid.
Last year Crutchlow, who lies fifth in the championship standings, missed last year's race after breaking his left collarbone in qualifying.
Spaniard Bautista (San Carlo Honda Gresini) clocked two minutes 3.303 seconds to top qualifying ahead of American Ben Spires (Yamaha Factory) and Australia's defending champion Casey Stoner (Repsol Honda).
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Championship leader Jorge Lorenzo (Yamaha Factory), who leads the standings by 20 points from Stoner, was fourth fastest.
Ducati Nicky Hayden and Valentino Rossi both suffered crashes at Vale corner during qualifying.
Hayden posted a time good enough for seventh on the grid before crashing out, while Rossi recovered from a crash at the start of the session to qualify in 10th.