Vettel came from too far back, and clumsily thudded into the side of Verstappen as sparks flew and the Ferrari auto spun around.
Hamilton won the downhill gallop to the opening bend, with Bottas slotting in behind, and Verstappen holding off Kimi Raikkonen's Ferrari.Lewis Hamilton has one hand, three fingers and a thumb on the world championship after romping to victory in Japan as his rival Sebastian Vettel finished a lowly sixth following a calamitous collision.
Marcus Ericsson crashed at Turn 7 early in the session.
Speaking of classic cars there were a few F1 versions on show in a pre-race display that included Mika Hakkinen back behind the wheel of a McLaren that steered him towards his first world championship at Suzuka in 1998. I don't regret the move, obviously with that outcome you would do it differently because with hindsight it's always easy. And he chose to go around the outside, he could have waited for me to understeer wide.
"I knew he had a penalty but I also felt that we were faster". Straight away I was much, much better than I've ever been through those particular corners.
"But I had a mistake so lost most of the time there but the second run we obviously didn't make it out on time because the rain came". Perhaps the stewards viewed the puncture as punishment enough, but in an incident-packed Japanese Grand Prix, this had the biggest potential for a serious accident. However, the Dutchman believed it had been a case of bad judgement on the part of his opponent.
Afterwards Verstappen said: "You can't overtake in that corner".
"For me it was a bit similar to China this year where I made the mistake".
As a result, both drivers came into the pits as soon as they possibly could, but not after wasting valuable time that they could have been using to try to record fast lap times. "With these new cars we are much faster than we were a year ago so just every time you come here the cars are getting faster and faster, the track is just incredible". But whether Vettel had an issue with his driver or he just loves the Ferrari Daytona that much, he decided half-way round to swap positions and continue his waving while behind the wheel of the 1960s auto.
"The team have done an unbelievable job this weekend and the call that we made to go out for Q3 was probably the most hard call", Hamilton said.
"But you can't really follow that close, and then we don't really have the top speed".
"We were trying to figure out what to do and the team were spot on with it".
He added: "It was a very tricky session today to get it right, we were debating Intermediates versus Supersofts for a long and we decided last minute - we had them ready and then we changed them - and then went out and got the timing flawless".