Ferrari's Charles Leclerc (25) will line up alongside Verstappen on the front row with teammate Carlos Sainz (28) and McLaren's Lando Norris (23), in a newly upgraded car, immediately behind.
The pole was Verstappen's fourth in a row, while Perez, already 69 points behind Verstappen after eight races all won by Red Bull, failed to make the top 10 for the fourth race in succession.
The Mexican had been second fastest in phase two of qualifying, held on Friday because of the sprint weekend format, but had three laps deleted for failing to stay within the track limits at turns nine and 10.
Drivers have another qualifying on Saturday for a standalone 100km sprint that no longer determines Sunday's grid under a new format introduced this season and first used in Azerbaijan in April.
Verstappen, winner of six races so far this season and chasing his fifth victory in a row on Sunday, said it had been hard to stay within the lines at Spielberg's Red Bull Ring, which has the shortest lap on the calendar in terms of time.
"We don't do it on purpose but with these speeds and the high-speed corners it's so hard to judge the white line," said the Dutch driver.
"It was about surviving ... it takes out the joy a little bit."
FASTEST TIME
Verstappen's fastest time was one minute 04.391 seconds, the double world champion claiming provisional pole with his first effort in the final phase and then going faster to make absolutely sure of pole.
Leclerc, winner in Austria last year for Ferrari's most recent victory, was a mere 0.048 slower in a big boost for the Italian team.
"It feels good to finally have a clean qualifying again and be back on the front row. The feeling has been a bit better in the last few races," said the Monegasque.
"I managed to put everything that I wanted in that last lap of Q3, very close to Max. Not enough today but overall I don't think we expected to be so close to the Red Bulls so it's a good step forward."
Seven-time world champion Lewis Hamilton (38) qualified fifth for Mercedes but teammate George Russell (25) will start 11th after also having a lap deleted in the second phase.
Canadian Lance Stroll (24) qualified ahead of double world champion teammate Fernando Alonso (41), for only the second time this season, with the Aston Martin pair sixth and seventh.
Nico Hulkenberg (35) will line up eighth for Haas, ahead of Alpine's Pierre Gasly (26), and Williams' Alex Albon (25) again impressively quick.
Dutch rookie Nyck de Vries (28) added to his woes, with speculation about his future at Red Bull-owned AlphaTauri growing louder, after qualifying in last place.
