The Mercedes driver, in dominant form all weekend at the Suzuka circuit, pumped in a one minute 27.760 second lap on the super-soft tires while it was still only just spitting with rain, Reuters reported.
Vettel and Ferrari teammate Kimi Raikkonen, who went out on intermediate tires in the final part of qualifying with the track still dry, lost time coming back in to fit the super-soft tires.
The German then made another mistake on his first flying lap and was unable to get another one in as the intermittent drizzle turned into a full-blown shower that drenched the track.
Meanwhile, Hamilton — who along with teammate Valtteri Bottas had gone out straight away on the super-soft tires to beat the rain — was lighting up the timing screens.
“The team have done an amazing job this weekend, and the call that we made for Q3 was probably the most difficult,” said the Briton, joined by Bottas on the front row after the Finn completed a second successive Mercedes front row lockout.
“It’s so difficult when the pressure is on to make the right call but that’s the big difference between us this year and that’s why we’re the best and the team deserve it,” added Hamilton.
Vettel trails his fellow four-time champion by 50 points in the standings with just four races left after Japan. His hopes are fading fast and he needs a huge stroke of luck now to reignite his challenge.
“Obviously it’s not the position we deserve to be in,” said the 31-year-old. “I think we have better speed than ninth but we’ll start there and see how it goes.
“Anything can happen tomorrow. Tomorrow is a new day.”