Vettel has a 90-point lead over Ferrari’s Fernando Alonso with only 100 still available and is almost certain to seal it at the next race in India.
Alonso was fourth, behind Webber and Lotus’s Romain Grosjean at Suzuka.
Vettel’s fifth win in a row came after a perfectly executed strategic race after falling to third at the start.
The German, who started second behind Webber, slipped to third at the start as Grosjean catapulted into the lead from fourth on the grid.
Vettel narrowly avoided front-wing damage after being clipped by Lewis Hamilton’s Mercedes on the run down to the first corner. The touch punctured Hamilton’s tyre, which damaged his rear bodywork and forced him into retirement.
Grosjean led through the first pit stops, with the Red Bulls measuring their pace behind.
When Webber stopped on lap 25 and the Lotus and Vettel stayed out, it became clear the Australian would be doing three stops and his rivals only two.
Grosjean made his second stop on lap 29 but Vettel waited a further eight laps and his controlled driving and the unmatched pace of the Red Bull meant he was only 2.1 seconds behind the Frenchman when he returned to the track.
On his vastly fresher tyres, Vettel took only three laps to catch and pass Grosjean heading down the pit straight to start lap 40, at the end of which Webber made his final stop, fitting the faster medium tyres rather than the hards his two rivals were using.
Webber was with Grosjean by lap 45 but found it much harder to pass the Lotus than Vettel had, finally managing it going into Turn One at the start of the 52nd of 53 laps.
Hamilton out after action-packed start
The time he lost ensured he was not able to challenge his team-mate for the lead, which might have been possible had Webber managed to pass Grosjean straight away.
“Ichiban, ichiban,” Vettel said on the team radio after the race – “number one” in Japanese.
“I’m blown away with today’s race,” he said afterwards. “I had a very, very poor start. I clipped a little bit the front wing, I couldn’t go anywhere.
“We looked after the tyres and had incredible pace towards the end and we managed to beat Romain and Mark towards the end.”
Vettel needs a top-five finish in India to be absolutely sure of the title, but will also seal it if Alonso scores no more than 10 points more than him.
Behind the leaders, Alonso had started eighth and moved up to sixth behind team-mate Felipe Massa at the start.
The Spaniard lost a further place to Hulkenberg when Sauber made an earlier first pit stop.
But he was able to pass Massa into Turn One on lap 26 after the Brazilian had cost himself time by going defensive into the chicane.
What makes Suzuka so special?
Hulkenberg held on to fourth through the second pit stops, but Alonso dropped back four seconds or so to conserve his tyres and then came back at the German later in the stint and passed him into Turn One on lap 46.
That left Hulkenberg to fend off Raikkonen, but the Finn finally took fifth place with a brilliant move around the outside into the chicane with just over two laps to go.
Hulkenberg’s team-mate Esteban Gutierrez scored his first F1 points with seventh to underline Sauber’s rise in form in the second half of the season.
Mercedes’ Nico Rosberg took eighth after a drive-through penalty following an unsafe release at a pit stop, ahead of McLaren’s Jenson Button and Massa, who lost ground with a drive-through penalty for speeding in the pit lane.