Lewis Hamilton took his seventh pole position in nine races this season at the first Tuscan Grand Prix.
Red Bull locked out the second row, Max Verstappen ahead of Alex Albon.
And Charles Leclerc gave Ferrari something to celebrate at their 1,000th grand prix with fifth place.
Bottas had topped all three practice sessions and Hamilton looked to be on the back foot heading into qualifying.
But Hamilton was quickest in the second session by 0.013secs and he extended his margin on the first laps of the top-10 shootout.
Hamilton did not improve on his final lap, and Bottas' hopes of doing so were dashed when Renault's Esteban Ocon had a spin and brought out yellow flags.
He said: "It has been really close this weekend. This is a really challenging circuit and Valtteri was quicker than me all day yesterday and this morning and even in Q1.
"I have been working really hard in the background to improve on my lines and set-up and I finally got the lap I needed.
"At the end, I think the wind picked up and I wasn't able to go any quicker. But I got the job done.
"It's crazy. You go through Turns Six, Seven, Eight and Nine at 180mph and the G-force is insane."
Bottas said he felt the Ocon incident had cost him his first pole position since the 70th Anniversary Grand Prix at Silverstone last month.
The Finn said: "I still had more and I was waiting for the time to get it right but I didn't get the opportunity. For sure it's disappointing."
Verstappen's margin in the Red Bull was the smallest it has been to pole position all year.