Hamilton had been quick in both Friday’s practice sessions but rain arrived on Saturday to disrupt his plans to pass Michael Schumacher’s pole record.
Qualifying was red-flagged after just seven minutes when Romain Grosjean spun off the start-finish straight and was not re-started for more than two hours.
But when the cars were allowed to race again, Hamilton was once again masterful and controlled his Mercedes around Monza’s high-speed corners with impressive skill.
Only Max Verstappen and Daniel Ricciardo, who qualified in second and third but will start well down the grid after engine penalties, could match anything like his pace.
And with Sunday’s day forecast, the Brit believes tyre management will play a huge role.
“Tomorrow depends on the weather,” Hamilton said.
“I heard it’s going to be dry so hopefully it’s a normal beautiful Italian day.
“It’s obviously going to be tough with the [tyre] temperatures but it’s great to see Red Bull up there, they did a fantastic job.
“I came across the line and I didn’t know if I had it but it felt like a good lap but I can’t believe. 69 [pole positions] – I’m so grateful.
“I love Italy.
“I’m so happy to be here even though we’re in Ferrari’s homeland we’ve got such great support for Mercedes.
“I really appreciate all the love.
“To do this here in such a historic circuit and beautiful country, I’m going to have some pasta tonight to celebrate.”
Verstappen echoed Hamilton’s concerns about tyre temperatures, even in the soaking wet conditions as the wet tyres struggled with the drier parts of the track.
“It was a tricky qualifying, sliding around a lot but also trying to cool down the tyres,” Verstappen said.
“But on my final run they worked pretty well so I was happy with second.”