The Gresini Honda rider, who grabbed his first pole in Barcelona this month, had been quickest in practice and made sure of the top slot on the grid with a lap of one minute 34.718 seconds.
Spies was a mere 0.009 off the pole pace.
Australia's championship leader Casey Stoner completed the front row on his works Honda with Yamaha's world champion Jorge Lorenzo in fourth place.
Italian Andrea Dovizioso put his Honda in fifth while Britain's Cal Crutchlow qualified an impressive sixth on the Tech3 Yamaha only two weeks after he broke his collarbone at Silverstone.
Italian MotoGP great Valentino Rossi qualified 11th on his Ducati.
Italian veteran Loris Capirossi was taken to the medical center for checks after falling in the session while Spaniard Toni Elias also crashed.
In the 125cc category, Spaniard Maverick Vinales qualified on pole for the second race in a row.
