Bezzecchi clocked the best time of one minute, 43.947 seconds to pip Pramac Racing's Martin by 0.043 seconds for his first pole since the British GP in August.
Bagnaia holds a 36-point lead over Martin in the overall standings, with Bezzecchi a further 29 points behind in third.
Luca Marini, Bezzecchi's team mate, qualified in fourth place ahead of factory Honda duo Joan Mir and Marc Marquez.
"I want to dedicate this pole to a friend of mine that unfortunately left us a couple of days ago."
Gresini Ducati's Alex Marquez has been ruled out of the remaining MotoGP weekend after suffering a double rib fracture in qualifying, his team said.
Persons:
Marco Simoncelli, Misano, Mooney VR46, Marco Bezzecchi, Jennifer Lorenzini, VR46 Racing, Jorge Martin, Francesco Bagnaia, Bezzecchi, pip Pramac Racing's Martin, Bagnaia, Martin, Luca Marini, Bezzecchi's, Joan Mir, Marc Marquez, Gresini Ducati's Alex Marquez, Hritika Sharma, Peter Rutherford
Organizations:
Marino, Marino Grand Prix, MotoGP, Rights, VR46, Ducati, Honda, Circuit, Thomson
Locations:
Marino Grand, Misano Adriatico, Italy, Rights NOIDA, India, New Delhi, Hyderabad