Valtteri Bottas took pole at the Emilia Romagna Grand Prix in Imola.
Red Bull's Max Verstappen qualified third, after a power unit scare in the second phase sent mechanics scrambling to fix his car, with AlphaTauri's Pierre Gasly a stunning fourth on the grid.
Mercedes need only a fourth place finish in Sunday's race to secure a record seventh successive constructors' world championship.
The pole, with a time of one minute 13.609 seconds, was a 13th in 13 races this season for the champions.
Sunday's race will be the first grand prix at Imola since 2006, with the track returning to flesh out a calendar ravaged by the COVID-19 pandemic, and the third in Italy this season.
"This track, when you push flat out, it's beautiful. I knew I had to improve in the last lap and I found those small gains that were needed," said Bottas, who was 0.097 quicker than Hamilton.
"It's a great feeling when you get those.
"It's going to be a good fight. It's one of the longest runs in the calendar into Turn One so no doubt Lewis and Max will be chasing me, but it's a good place to start and hopefully the pace is good."
Hamilton leads Bottas by 77 points, having won eight times so far this season, and is closing on a record-equalling seventh drivers' title although he will have to wait at least until Turkey in two weeks' time for a chance to clinch it.
"Valtteri did a great job. It was a pretty poor lap from myself. These things happen, you can't always get it perfect," said Hamilton, who had been quickest after the first flying laps in phase three.
