Bagnaia, who leads Jorge Martin by 62 points in the overall standings, finished top with a time of one minute 38.639 seconds at the Circuit de Barcelona-Catalunya.
"This is one of the most important pole positions as Aprilia are so strong," Bagnaia said.
Aprilia's Aleix Espargaro, whose record Bagnaia broke, set the second-fastest time after dominating practice on Friday, while Portugal's Miguel Oliveira (RNF Aprilia) came through the first qualifying session to complete the front row.
"I tried my best but I felt a lot of chattering, I don’t know if it was because of the temperature or the low fuel in the tank, but I couldn't quite get where I wanted to go," Espargaro said.
"Anyway, congratulations to (Bagnaia), this is MotoGP, it's tough, and the front row or the first two rows is more than good enough."
Spaniard Maverick Vinales (Aprilia) was fourth, with Pramac Racing duo Martin and Johann Zarco in fifth and sixth.
Yamaha's Fabio Quartararo, the 2021 world champion, did not advance to the second qualifying session after falling over in the gravel.
