Webber clocked a time of 1 minute, 30.975 seconds at the Suzuka circuit, with Vettel just under two-tenths of a second behind in second place after struggling with his KERS power-boost system.
"Sebastian had a problem so it's a bit of a hollow pole but you have to grab the opportunities when you can," said Webber, who is leaving F1 at the end of the season. "It's a very nice farewell for me on my final time here at Suzuka and on a phenomenal circuit. It was a real highlight for me. In general we've got a good car for the race."
Mercedes driver Lewis Hamilton was third fastest, followed by Lotus' Romain Grosjean and Ferrari's Felipe Massa. Mercedes' Nico Rosberg was sixth ahead of Sauber driver Nico Hulkenberg.
Vettel has won three of the past four races in Japan and can clinch his fourth successive world title in Sunday's race. The title will be his if he wins and nearest rival Fernando Alonso, who was eighth in qualifying, finishes ninth or worse.
Vettel is looking to join Michael Schumacher and Juan-Manuel Fangio as the only men to win four championships in a row. The German, who has a 77-point lead over Alonso, has won the past four races, leading after every lap in each of them.
Vettel, who was bidding for his fourth straight pole, was hobbled by a KERS problem on his first lap of the final qualifying session but refused to blame Saturday's finish on his car's technical problems, which initially surfaced in the morning practice.
"We had a technical problem this morning but I don't think that made a difference in finding the rhythm," Vettel said. "As a fact, we are on the front row which is a great result for the team."
Despite the championship title being on the line, Webber said there was no chance of him intentionally moving aside to help his teammate.
"It's not as though it's the last race of the year," Webber said. "He has a big lead in the standings so in general we'll be racing for ourselves tomorrow."
Lotus driver Kimi Raikkonen qualified ninth while McLaren's Jenson Button, who won here in 2001, round out the top 10.
The first session of qualifying was noteworthy for a couple of fires.
Flames leapt out of the back of Esteban Gutierrez's Sauber when it was inside the garage, forcing the Mexican to hastily jump out of the cockpit, but they were quickly extinguished and he was soon able to get back on the circuit.
Jean-Eric Vergne's Toro Rosso came to a halt with flames coming from both rear brakes, with the resulting smoke resulting in a red flag which temporarily halted the session.
The Grand Prix Drivers Association said in a statement the drivers will honor Maria de Villota with a moment of silence before Sunday's race after the former F1 test driver was found dead in a hotel room in Seville, Spain, on Friday. Her family said an autopsy showed that lingering injuries from her racing accident a year ago likely caused her death.