Spaniard Martin began with a scorching lap of one minute 30.832 seconds, bettering Marco Bezzecchi's (24) previous record set during practice on Friday, before topping the timesheets by improving on his own mark with a time of 1:30.390.
"It was a great lap, a great weekend overall. I was a bit worried about today," Martin said.
"But then I went all-in on the lap, I was braking super-heavy in some corners. I took a lot of risks to take the pole position, I'm so proud of my team and also myself."
Bezzecchi, nursing a wrist injury, kept up his pace from Friday to take second spot, while Ducati's MotoGP world champion Bagnaia, who had his leg run over in a crash at the Catalan Grand Prix, ended third.
"I don't know what Jorge did today, it's something incredible, if he does the same in the race it will not be easy," said Bagnaia, who could be seen limping after getting off his bike.
"I'm so pleased to be in the front row, considering the pain I'm feeling and where we were just five or six days ago."
The three riders occupy the top three spots in the overall standings, setting up an exciting weekend at the Misano circuit on Italy's Adriatic coast. Bagnaia is top with 260 points, with Martin (210) in second and Bezzecchi (189) in third.
Yamaha's Fabio Quartararo (24), the 2021 world champion, did not advance to the second qualifying session after finishing third-fastest in Q1.
Italian Enea Bastianini (25), who underwent surgery in Modena on Monday after fracturing his left hand and ankle at the Catalunya GP, will miss Misano as well as upcoming races in India and Japan.
