Mark Webber started on pole but ended up second as his Red Bull team-mate's decision to pursue a two-stop strategy proved critical at Suzuka.
Romain Grosjean drove a brilliant race to come third, while Fernando Alonso's fourth place finish ensured that Vettel will have to wait at least one more race to lift yet another title, with the German 90 points clear of his Spanish rival with four races left.
"Ichiban (first), Ichiban," Vettel shouted in Japanese over the team radio, whooping in delight after taking the chequered flag at the end of a race that hinged on his ability to do two stops to Webber's three.
Japanese Grand Prix
Japanese GP: final grid line-up
"Great job, thanks a lot for bringing the car back, unbelievable. You're the best team in the world. Thank you very much boys, I love you."
It was Vettel's fifth win in a row, ninth in 15 races this season and 35th of his career.
Asked on the podium about the championship, with the passionate crowd roaring in approval, he added: "Obviously we have a very good gap but we still keep pushing... it looks very good at this stage but it's not over until it's over."
Alonso, who became Formula One's leading all-time points scorer, had no illusions about his chances.
"Even if Vettel doesn't finish all of the races I need to win nearly all (of them), so it's a matter of time," said the Spaniard.
Vettel started second on the grid but made an awful start, dropping places at the beginning of a race for the first time this season.
That bad start proved fateful for Lewis Hamilton as well, with Vettel hitting Hamilton's rear right tyre, puncturing it instantly. Hamilton limped back to the pits with shredded rubber, but as he did so he sustained car damage that would spell the end of his race.
"The floor was destroyed... I was a second and a half to two seconds off the pace and the car was pulling to the right. It's a good job they pulled me in," said 2008 world champion Hamilton.
It was Grosjean who impressed most at the start, however, jumping from fourth into the lead and taking a firm grip on proceedings early on.
He and Webber pulled clear, though Vettel stayed in touch as the middle phase of the race became a procession with drivers trying to save tyres.
Vettel proved the master at looking after his rubber: he made a late first stop, and then ran a very long second stint which got him ahead of Grosjean and to within 15 laps of the chequered flag.
With Webber was forced to stop once more, Vettel took a lead that he would not relinquish.
Grosjean was expected to stop again as well, but gambled on staying out for a 24-lap final stint to try and secure second place ahead of Webber.
It almost paid off as the Frenchman defended brilliantly, but Webber finally got past the Lotus on the penultimate lap.
"Mark was going through the tyres a bit quicker and getting into trouble earlier," said Red Bull principal Christian Horner. "It made a huge amount of pressure on the two-stop and would have been very difficult to beat Grosjean so we switched from two to three.
"Unfortunately we lost too much time at the end there behind Grosjean for him to have a crack at Sebastian but he (Vettel) just made the tyres last extremely well."
Kimi Raikkonen was fifth for Lotus with Nico Hulkenberg sixth in the Sauber.
Sauber's Mexican Esteban Gutierrez became the first rookie driver to score a point this season with seventh place for Sauber.
Nico Rosberg put some points on the board for Mercedes, who slipped further behind Ferrari in third place in the championship, with Britain's Jenson Button ninth for McLaren. Ferrari's Felipe Massa was 10th.
The day belonged to Vettel, however, and with his championship lead over Alonso now stretched to 90 points, the German is now odds-on to win a fourth consecutive world title in India in a fortnight's time.
Japanese Grand Prix
Japanese qualifying press conference
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