Ferrari's decision to begin Q3 on intermediate tyres instead of supersofts backfired spectacularly as the rain they expected held off just long enough for Hamilton to set a fastest lap of one minute, 27.760 seconds - three-tenths quicker than teammate Valtteri Bottas.
Lewis, who leads Vettel by 50 points with five races left this season, led a Mercedes front-row lock-out and will start as the hot favourite to tighten his stranglehold on the Formula One championship in Sunday's race at Suzuka. He was up to sixth by the third corner, passing both Toro Rosso, then fifth when he passed Romain Grosjean's Haas into Spoon.
The resulting collision sprayed debris across the track and resulted in a puncture for the Haas driver on the run down to Turn 1 - and ultimately a Safety Car to clean up the mess.
The four-time world champion was in a class of his own to lead Mercedes one-twos in both sessions as Ferrari and Red Bull failed to match his pace.
Vettel came from too far back, and clumsily thudded into the side of Verstappen as sparks flew and the Ferrari vehicle spun around.
"When you get in the auto it's just the best, it's so much fun and I'm truly grateful to have the opportunity I have".
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Verstappen was already carrying a five-second penalty for forcing Vettel's team mate Kimi Raikkonen off the track earlier in the race and would have dropped behind Vettel anyway at the pitstops.
"Keep him [Bottas] under pressure, keep it clean".
It was a disappointing afternoon for Red Bull's Daniel Ricciardo who ended up 15th after failing to set a time in the second qualifying, heading into the pits at the end of his outlap with what appeared to be an engine problem.
Arrivabene would not rule out making changes to Ferrari's organisation as a reaction to the errors of late.
Driver of the day Tricky one, this. I think we have a better speed than ninth, but we start there and then we see how it goes. Hamilton was supreme, driving superbly and overshadowing Bottas in what has become in recent races a dominant auto. Judgement reservedWhat happen next?
"The team have done an incredible job this weekend and the call that we made to go out for Q3 was probably the most hard call", Hamilton said.
Mercedes's brilliant use of team orders - controversial as they may be - made the title all-but impossible for Vettel last weekend, and his disappointing showing here combined with yet another pole for Hamilton suggests that tomorrow's race might underline that.