Zarco, 30, was involved in a high-speed crash with Morbidelli, 25, at turn three in Spielberg, with their cartwheeling bikes missing Yamaha duo Valentino Rossi and Maverick Vinales by inches.
Zarco and Morbidelli were summoned to a stewards' meeting at the track on Thursday to discuss Sunday's accident.
"After evaluation it was determined that there was evidence of irresponsible riding from Johann Zarco, which has resulted in a penalty. The Frenchman will start his next race from pitlane," MotoGP said in a statement.
Some rivals had blamed the Frenchman for taking an unusual line while braking into turn three, although Zarco denied making a deliberate move.
Zarco fractured his wrist in the crash and required surgery. He will miss Friday practice at the Styrian Grand Prix in Austria but still hopes to race on Sunday. (Reporting by Arvind Sriram in Bengaluru; Editing by Mark Potter)