Vettel is now on the cusp of becoming only the third driver in F1 to win a fourth consecutive world title, standing alongside two of the greats in Michael Schumacher and Juan Manuel Fangio.
Setting a personal best record of five successive wins, and a fourth in the last five years at Suzuka, Vettel is now 90 points clear of the only man mathematically capable of catching him.
With Fernando Alonso finishing fourth, it means the champagne is on ice for another fortnight until the Indian Grand Prix where Red Bull should also celebrate their fourth straight constructors' crown.
For Vettel, standing on top of the podium at Suzuka summed up why he is in F1 because after the boos at Monza and in Singapore, there were nothing but cheers and adoration from the knowledgeable Japanese fans
Offered a choice between going down in history with Schumacher and Fangio, or standing on top of every podium on the calendar, Vettel replied: "I prefer the second thing."
The 26-year-old German added: "When I was small I dreamed about F1, and honestly never thought one day I would be able to test one of these cars.
"The first time I did I s*** myself the first couple of laps and I thought 'All right, that's for real men, not for me', but then I got used to it and obviously wanted to do more.
"A couple of years later Red Bull gave me the chance at Toro Rosso to get some races, and it's incredible what's happened over the last couple of years.
"But nothing has changed in the way I still love racing, I love the challenge, I'm still nervous when I wake up on Sunday, still excited when I walk on the grid and tense, looking forward to the race.
"I enjoy - not the numbers - but the fact I'm racing, and a great crowd today, a fantastic day.
"It would be a shame if you were too tense and if you tried to force things too much, so you have to allow yourself to enjoy it because this (the job) is not normal. It doesn't happen to everyone.
"I'm very fortunate I'm one of 22 guys in Formula One, that when we leave our hotels we get great respect from the fans who are cheering, shouting our names, and it's just great.
"That's what I look forward to most, and obviously trying to do it again - and I love trophies so I don't mind collecting a few either."
On a circuit Vettel has made his own over the years, he suffered a rare poor start behind polesitter and team-mate Mark Webber.
That allowed Mercedes' Lewis Hamilton a chance to squeeze between them, only to sustain a right-rear puncture after the merest of touches with the left end of Vettel's front wing.
Hamilton was eventually forced into retirement with severe damage to the floor of his car after he had limped back to the pits.
Instead, from fourth on the grid, Lotus' Romain Grosjean grabbed the early lead, and from that moment it became a battle of strategies.
On a two-stop, and exercising patience over the opening laps, Vettel made his work to perfection to finish seven seconds ahead of Webber, who stopped three times, and Grosjean who changed tyres twice.
"I've now won four times here at Suzuka, which is incredible," added Vettel.
"Regarding the championship we have a very, very good gap. It looks very good at this stage, but we will still keep pushing. It's not over until it's over."
As far as Alonso is concerned, the Spaniard knows "it's only a matter of time before he (Vettel) will be champion".
Alonso, who finished 45 seconds down, added: "We have different goals now. We will continue to try to do out best on Sundays, and when it is mathematically settled we will congratulate him."
Lotus' Kimi Raikkonen was fifth, followed by the Saubers of Nico Hulkenberg and Esteban Gutierrez, the latter in the points for the first time in his rookie year.
Mercedes' Nico Rosberg, given a drive-through penalty for an unsafe release after almost colliding with McLaren's Sergio Perez, was eighth.
McLaren's Jenson Button and Felipe Massa in his Ferrari completed the top 10, with Paul Di Resta 11th for Force India.