The 35-year-old Yamaha rider, nine-times a world champion in all categories, ran wide and fell heavily early in the race at the Motorland Aragon circuit.
"Valentino suffered a concussion with a suspected loss of consciousness. From a neurological point of view he has recovered very well," said MotoGP medical director Michele Zasa in a statement issued by Yamaha.
"He was taken to hospital in Alcaniz to make a further check, in particular a CT scan of the skull that has ruled out any bleeding in the brain.
"As a precaution he will be observed in the coming hours, but there are no special reasons for concern," added the statement.
Rossi had won the previous round at his home Misano racetrack and had been hoping for another podium finish in a rain-hit race eventually won by Spanish team mate Jorge Lorenzo.
Image: Valentino Rossi
Photograph: Albert Gea/Reuters