The second row was filled by the Red Bulls of Max Verstappen and Alex Albon, the latter with one of his best performances of the season.
After 24 minutes, however, Hamilton trimmed the best time by just 0.022 seconds to top Bottas before Verstappen, on mediums, clocked 1:17.116 to take control for Red Bull, the Dutchman exploiting his car's handling on the high-speed corners of the picturesque circuit.
"It's been a really tough weekend, if I'm honest", said Hamilton.
"That's why I have so much respect for all these drivers because it's not only the ability to drive but to understand those things and to be engineers, at the end of the day". I felt I was breathing heavier at the ends of the lap.
"The whole body is completely tense and every muscle is fully engaged".
Vips was hit with the injunction after being found to have impeded Swiss driver Louis Deletraz (Charouz) in the qualifying session Friday. The circuit is narrow and overtaking will be extremely hard.
All of which suggests Hamilton's pole will be vital for him to take the 90th win of his career, one short of Michael Schumacher's record.
"I have been working so hard in the background to improve on my lines and my set-up".
Hamilton is 47 points clear of Bottas in the standings and the Finn needs to pull out something special to rein in the Briton.
"That's why we made a decision to run a unique livery on the cars for this event, with the SF1000s taking to the track at the Mugello Circuit in the Burgundy colour first seen on the 125, the first racing auto to carry the Ferrari name". The only team to have competed in the world championship since the inaugural season in 1950, they have won 16 constructors' titles and 15 drivers' championships.
Sebastian Vettel finished a lowly 18th for Ferrari, with the four-time world champion now facing the prospect of an embarrassing Q1 elimination for the second week in succession.
In addition, Mick Schumacher, the son of Michael Schumacher, Ferrari's and F1's most successful driver, will do a demonstration run on race morning in his father's final championship-winning auto, the F2004. His teammate, Lance Stroll, was in seventh.
Lando Norris was in 11th for McLaren and Daniil Kvyat in 12th for AlphaTauri.
Lance Stroll was fourth for Racing Point ahead of last weekend's Monza victor Pierre Gasly of Alpha Tauri and his Racing Point team-mate Sergio Perez, who is due to be replaced next year, when the team is renamed as Aston Martin, by four-time champion Sebastian Vettel.