Rain began to drizzle onto the Suzuka Circuit late in Q2, and Ferrari tried to pre-empt a heavier downpour by sending both Vettel and Kimi Raikkonen out on the intermediate tyre for the top-10 shootout.
It was the only team that went for the wet-weather rubber, however, and it immediately became obvious to the Italian team that it had erred in its strategy.
As the Scuderia reeled, Hamilton put his car on provisional pole with a 0.3-second margin to Bottas in second, and Red Bull Racing’s Max Verstappen slotted into third.
Vettel and Raikkonen dashed back to the pits to switch to the supersoft tyre, but as they emerged from pit lane on fresh dry-weather rubber, the heavens finally opened, coating the track with enough rain to make it borderline undriveable on slicks.
Raikkonen managed to get himself up to fourth place, albeit 1.7 seconds off the pace, but Vettel struggled in the conditions, running wide onto the saturated kerbs on his first flying lap to set the ninth-quickest time and almost crashing into the bridge at the exit of the second Degner on his second attempt.
Ferrari was forced to abandon, and with Bottas unable to better his original lap in the rapidly deteriorating conditions, Hamilton claimed his 80th Formula One pole position.
“I can’t believe I have 80!” said Hamilton. “I couldn’t have done this without the team.
“It’s really just such an honour to race for this team, for the guys. I’m just so thankful.
“I’m so proud to be on this journey with them. I never in a million years thought I would get to 80.”
Reflecting on Ferrari’s tyre strategy at the beginning of the session that handed the team an uncontested front-row lockout, Hamilton paid tribute to the experience of his Mercedes pit wall.
“The call that we made to go out in Q3 was probably the most difficult call. The team were just spot on with it and gave us the opportunity to grab this pole position.
“It’s so difficult out there to make the right call, but that’s another real big difference we as a team have made this year.
“Every team has smart people, but when it comes to being under pressure, making the right decision, the right calls, that’s why we’re the best team in the world.”
Valtteri Bottas qualified second and put the 0.3-second gap to his teammate down to a mistake in the final sector, but Max Verstappen was ecstatic to qualify third for Red Bull Racing.
“I think realistically normally we would be close to Ferrari but it would be hard to beat them,” he said. “But we made the right call in Q3, and I’m very happy to be third.”
His teammate, Daniel Ricciardo, was knocked out in 15th with power unit troubles.
Raikkonen qualified fourth ahead of Haas’s Romain Grosjean, but the home Japanese fans were most enthused about the Honda-powered Toro Rosso cars qualifying sixth and seventh, with Kiwi Brendon Hartley beating Frenchman Pierre Gasly by 0.005 seconds.
Force India’s Esteban Ocon and Sergio Perez qualified eighth and 10th, split by the downtrodden Vettel in ninth.
The clouds began to blacken over the Suzuka Circuit for the beginning of Q2, but the rain stayed away for the opening laps, allowing Mercedes to forebodingly set the two quickest times of the segment with the more durable soft tyre while the rest of the field used the fastest supersoft compound.
Ferrari was worryingly 0.3-seconds off the pace, but the picture was worse for Red Bull Racing, with Daniel Ricciardo returning to his garage with a power unit problem before he was able to set a lap.
The Australian’s mechanics worked furiously to identify and fix the problem, but they were beaten by the rain, which essentially ended the session. Ricciardo furiously climbed from his car, swearing loudly from inside his helmet.
Charles Leclerc attempted to put his Sauber into Q3, but he spun his car on his final flying lap as the rain arrived, leaving the Monegasque stranded in 11th.
Kevin Magnussen was eliminated in 12th for Haas ahead of Renault’s Carlos Sainz and Williams’s Lance Stroll.
Daniel Ricciardo was classified 15th without a time.
Marcus Ericsson disrupted the session eight minutes in with a big crash at the Dunlop curve.
The Sauber driver, who will be replaced by Kimi Raikkonen at the Swiss team next season, ran wide as he crested the top of the turn-seven exit and lost control of his car, careering out of control through the gravel and smacking rear-first into the barrier.
The top six cars didn’t feel a need to improve their first attempts set before the crash, turning the rest of the session into a pure midfield shootout to avoid elimination.
With Ericsson out of the running, practice pace suggested both McLaren and Williams would occupy the rest of the drop-zone positions, but Canadian Lance Stroll sprung a surprise by beating Renault’s Nico Hulkenberg to P15.
Hulkenberg had crashed at the end of Saturday morning practice but had little difficulty making it out for qualifying; however, Renault has been struggling throughout the weekend, leaving it vulnerable in the tightly contested midfield battle.
Stroll’s Williams teammate, Sergey Sirotkin, qualified 17th ahead of McLaren duo Fernando Alonso and Stoffel Vandoorne, the former outqualifying the latter for the 22nd consecutive occasion.
Marcus Ericsson was classified 20th.