That will put the two finest drivers of their generation on the same amount of titles and, given the strength of both Mercedes and Ferrari, it sets up a tantalising battle in 2018 as one of them would have the chance of moving level with Juan Manuel Fangio's career tally of five - now the second-best in F1 history.
Hamilton, who leads the German by 34 points with just five races to go, brushed aside a suggestion about how aggressive Vettel might be into the first corner.
Hamilton is the only driver to finish in the points at every race this season, winning eight races and finishing on the podium three other times.
Hamilton, who started the Japanese grand prix from pole position, can clinch the 2017 title at the USA grand prix in Austin later in October.
"It is normal to be critical, especially when things go wrong", said Vettel, of his Ferrari team.
Ferrari's continuing reliability woes have robbed Formula One fans and Mercedes of the thrilling battle they had been hoping for, last year's world champion Nico Rosberg said on Sunday.
"Of course it hurts, and we're all disappointed", said the four times world champion, who hugged his mechanics and gave the crowd a quick wave after returning to the pits. "I then had Valtteri coming at the end, so to have a bit of pressure at the end made it more exciting - it was good fun". "I just need to keep my head down".
"I could have only dreamed about having such a gap in the standings".
"With the VSC towards the end, I lost a lot of temperatures in the tires and waking them up was not so easy".
"I got stuck behind traffic, I was losing so much time and Max' vehicle was so big in my mirror".
Bottas had stayed out long, having opened with the soft tyre after his five-place grid penalty and had inherited the lead through the stops but Hamilton was being held up by his team-mate and it allowed Verstappen to close the gap to under a second.
With his main rival out, all Hamilton needed to do was to stay clear of any incidents and drive a low-risk race.
Today's result marks the tenth victory for the Mercedes-Benz Silver Arrows of the 2017 season.
The Briton emerged from the pitlanes just ahead of the Red Bull in third, and retook the lead when Ricciardo pitted, and his slower teammate Bottas moved aside shortly after while keeping the threatening Verstappen at bay in third.
Hamilton also won his maiden pole at the Suzuka and he did it in style by smashing Michael Schumacher's circuit record of 1:28.954s by clocking a fastest lap of 1:27.319s in the qualifying on Saturday. Whether Max could have passed Lewis if these two backmarkers hadn't been there is a question we'll never have answered, but given the pace differential we saw before the leaders encountered these two, you wouldn't have bet against it. "It's been a really good day and every lap was fantastic".