With all eyes on the runaway championship leader, who could secure a fourth successive world title tomorrow, the soon-to-retire Australian lapped in 1min 30.915secs to push Vettel into second on the grid.
Lewis Hamilton's Mercedes will start behind the Red Bulls on the second row alongside Lotus's Romain Grosjean, with Felipe Massa and Nico Rosberg on the third rank.
Nico Hulkenberg timed seventh, just ahead of Ferrari's Fernando Alonso. If Vettel wins on Sunday, the Spaniard will need to finish inside the top eight to keep the title race alive.
Webber is quitting Formula One at the end of the season. But he said pole position was a sweet farewell to pacy Suzuka, despite the advantage of Vettel driving without his speed-boosting Kinetic Energy Recovery System (KERS).
"Sebastian had a problem so it's a little bit of a hollow pole," the 37-year-old told reporters. "But you take them where you can get them. It's not like they hand them out. You've still got to put the laps in.
Webber pulled no punches when asked if he would let Vettel pass him if asked on Sunday.
"He'll do his race tomorrow and I'll do my race," insisted Webber. "Seb's had a phenomenal year. It's not like it's the last race of the championship... In general we'll be there for ourselves tomorrow."
Vettel refused to blame his technical issues for missing out on what would have been a fifth straight pole in Japan and his fourth in a row.
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