Hamilton's win means he only has to beat Vettel by eight points to win the championship.
It seems odd that a team which was unbeatable more than a decade ago hasn't won a driver's Championship since 2007, despite being the most recognizable name in Formula One history.
Despite Ferrari locking out the front row with what seemed a faster auto, Hamilton won after passing Vettel on the opening lap and then Kimi Raikkonen after chasing down the leading Finn.
The victory was the 71st of his career, leaving him only 20 behind the record of seven times world champion Michael Schumacher.
"In terms of Sebastian's performance..."
Vettel, who had started eighth after a failed tyre gamble in qualifying, was trying to pass the young Dutch driver for third place at the fast left-handed sweep of Suzuka's Spoon corner. He resumed in 19th place with a damaged auto.
Stewards reviewed the Verstappen contact and took no action. I saw a gap and went for it on the inside, he obviously tried to defend and I couldn't go anywhere, so we touched.
However, Vettel said Verstappen was "completely to blame" for the incident.
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That incident brought late drama, but after the thrills of the four meetings last season, this was something of an anti-climax. We can play ball to the forward most of the passes to defenders. boring game poor performance.
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Correspondent Daniele Sparisci said the former president was the "custodian of internal balance", and in the absence of that, Ferrari has split into two warring factions. And as soon as he realises somebody is close or next to him he tries to, in my opinion, push when you shouldn't push any more.
He was penalized five seconds and could well have finished second without it, having crossed the line 1.3 seconds behind Bottas.
"In that corner you can not overtake", he said.
Asked if he felt he could claim credit for "breaking" Ferrari, Hamilton said it has been a team effort: "I think together we can claim credit for applying the pressure, and ultimately maybe that's what happens in head-to-head battles with top competitors - eventually someone has to, even though they're still performing great, one of them can't always be performing the same".
Force India's Sergio Perez was seventh ahead of Haas driver Romain Grosjean.
Honda-powered Toro Rosso were unable to convert their impressive qualifying in the manufacturer's home race into points.
There was a short safety-car intervention to clear up debris left by a collision between Kevin Magnussen's Haas and Charles Leclerc's Sauber and bodywork strewn around the lap by the Dane as he returned to the pits with a puncture.
For one reason or another, this partnership just isn't working out and fans are beginning to get fed up with the mismanagement and strategical errors coupled with silly mistakes by one of the sport's most recognizable faces, which leaves just one thought in mind - maybe this pairing was destined to fail from the very beginning?