The Australian was 0.174 seconds quicker than Vettel in qualifying, the German having suffered a power-boost system failure that cost him in the region of 0.3secs a lap.
Red Bull team principal Christian Horner left all options open when asked after qualifying whether the drivers would be free to race.
"They race for the team," Horner said. "They're free to race and the goal is to do the best they can for the team."
Vettel and Webber - best of enemies
Vettel added: "It's unfortunate these things come up when it is the end of the season but these sorts of questions come up because one car is in a strong position.
"We will try our best. I'm sure we'll try hard and race hard like we did in the past."
Vettel has won eight of this season's 14 grands prix, including the last four races in South Korea, Singapore, Italy and Belgium - a dominance Britain's Lewis Hamilton has said
risks driving fans away.
Nico Rosberg of Mercedes and Ferrari's Fernando Alonso - who qualified in sixth and eighth respectively in Japan - have two wins apiece, while Webber has none to his name in 2013.
Hamilton, one of the other two drivers to manage a race win this year, will start third on the grid on Sunday in his Mercedes, with fellow Briton Jenson Button of McLaren 10th.
Japanese Grand Prix, day three
Sunday 13 October : Race coverage at 06:00 BST (BBC One) & 06:55 (BBC Radio 5 live), plus live text commentary online. F1 Forum: 09:15 on BBC Red Button. Highlights: 19:00 on BBC Three & BBC Red Button
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