The 25-year-old Ducati rider was judged to have handicapped Alex Marquez during free practice in the morning.
A MotoGP motorcycle statement said Bagnaia was found “going slowly on the race line, causing a dangerous situation for the other occupants.
“There can be no appeal, which means that the decision is final,” the statement added.
Italy’s Bagnaia finished second after two sessions of practice on Friday, 0.114sec behind compatriot Enea Bastianini as Ducati bikes took the top four places at Misano.
Championship leader Quartaro finished fifth, 0.326 seconds off the lead, after leading the times in today’s morning practice session.
Yamaha’s Quartararo, also world champion, leads third-placed Bagnaya by 44 points in the overall standings.
Bagnaia’s teammate Jack Miller was third, 0.185 seconds behind Bastianini, while Aprilia’s Alex Espargaro, who is 32 points behind Quartararo in the championship, was seventh with 0.412 seconds.