He was taken immediately to the medical centre, where doctors were able to pop his shoulder back into place.
It is not yet clear whether he will be able to take up his pole position for today's British Grand Prix.
The Spaniard, chasing a fifth consecutive win, fell at Vale late on in warm-up.
Cal Crutchlow had also fallen at the same spot moments earlier, and the Briton had to run to safety - as did five marshals surrounding his bike - as Marquez's Honda ploughed straight into the Tech 3 Yamaha.
Marquez had thankfully separated from his bike, but tumbled through the gravel and immediately clutched his left shoulder as he rose to his feet.
Should he be unable to race he is guaranteed to still lead the championship given his current 26-point advantage.
Marquez is currently undergoing examination and treatment. His fitness will be reviewed before the race.
His chief rivals Jorge Lorenzo and Dani Pedrosa have also suffered massive crashes in similar cool conditions during the season.