The Briton's Finnish team mate Valtteri Bottas will line up alongside on the front row of the starting grid for Sunday's race, when conditions are expected to brighten up, with Ferrari's Kimi Raikkonen and Sebastian Vettel behind.
Hamilton now has 77 career poles, and five this season, but Saturday's went against the odds with the opportunity emerging as the heavens opened.
"It's great for the team to have a one-two. We couldn't have expected this," said the 33-year-old, who leads Vettel by 17 points after 11 races in the battle of four times world champions.
"Ferrari have been quickest all weekend and we were doing our best to catch up, but then the heavens opened and it was fair game.
"It's so tricky out there, at the beginning it was dry and then it got wetter so it was hard to say how much grip we had."
Vettel had been fastest in Friday and Saturday practice, with track record times, and Red Bull also expected to be in the mix but Australian Daniel Ricciardo failed to make the cut in a tricky second phase and starts 12th.
Dutch team mate Max Verstappen qualified only seventh, with Renault's Carlos Sainz and Toro Rosso's Pierre Gasly fifth and sixth respectively.
(Reporting by Alan Baldwin, editing by Toby Davis)
