Bagnaia takes Czech MotoGP pole as Marquez crashes
Bagnaia, on a Ducati, had to go through qualifying one after a slow start in Brno but regained composure to earn his first pole position of the season.
"Luckily I had this 15 minutes more in qualifying. Then I understood better the way to push in this track," he said.
"We just did a little adjustment that helped a lot," the 2022 and 2023 world champion added.
Marquez will start from the second spot after losing control at turn 13 in the last qualifying lap -- a blow for the Spaniard as split times suggested he would top Bagnaia easily.
He blamed Frenchman Johann Zarco's crash in the same sector moments earlier for a loss of attention.
"When Zarco crashed, I saw some smoke and then my vision went a bit there and I went a bit wide and I just lost the front," said Marquez.
"But apart from that I'm happy with that second position."
Frenchman Fabio Quartararo on a Yamaha will complete the front row.
Reigning world champion Jorge Martin will start from the fourth row on his return after a series of injuries.
Martin sat out the first three races following two pre-season crashes and when he returned at Qatar in April, he crashed heavily again and missed the next seven races.
Marc Marquez, who has taken seven pole positions so far this season, leads the championship with 344 points after 11 of 22 races.
His younger brother Alex is second with 261 points and Bagnaia is third with 197.
Bagnaia smashed Marquez's Brno lap record from 2016 by over two seconds, clocking 1min 52.303sec.
Returning to the MotoGP circuit after a five-year break due to financial woes, Brno has welcomed riders with a brand new, faster tarmac.
Marquez won the last four grand prix, taking the honours in both the sprint and the main race each time.
He is eyeing his seventh MotoGP world title -- and first since 2019 -- that would put him level with the legendary Valentino Rossi.