Vettel, a two-time winner in Japan, secured his fourth consecutive pole at Suzuka and will be in a good position in Sunday's race to further erode the championship lead of Ferrari's Fernando Alonso.
"We had a very smooth qualifying session, nearly perfect," Vettel said. "The car felt perfect from the start. We didn't have a great result yesterday so I'm very happy with today's session."
Vettel won the previous race in Singapore and is just 29 points behind Alonso in the standings with six races left. The German has always performed well at Suzuka, winning here in 2009 and 2010 and taking third place last year to wrap up his second consecutive drivers' championship.
Alonso qualified seventh, and all of Red Bull's championship rivals will start the race several places back after a yellow caution flag in the final moments of qualifying prevented them getting in a last flying lap.
Lotus driver Kimi Raikkonen, third in the standings, caused the yellow flag when he spun at the edge of the track, and qualified eighth, while McLaren's Lewis Hamilton obeyed the flags and slowed, qualifying ninth.
"I spun. I was on a good lap and I was pushing — maybe a little too hard — and lost the rear," Raikkonen said. "It's a shame as the car feels the best it has all weekend. If the car's good tomorrow we should be able to move forward. Let's see what happens."
Hamilton's McLaren teammate Jenson Button qualified third but will start eighth due to a penalty for replacing the gearbox in his car.
"It's going to be tough tomorrow," Button said. "Never say never, and we will have a good car for the race tomorrow."
Hamilton, who is fourth in the standings and needs a good result in Sunday's race to avoid losing ground, said he was unhappy with Saturday's qualifying.
"Today's qualifying session was one of the most disappointing of my year," Hamilton said. "To be honest, I went the wrong way with the set-up and ended up with too much understeer. Until qualifying, the car had felt great all weekend, but I just couldn't make it turn this afternoon, and as a result I just couldn't extract the best from it."
Mercedes driver Michael Schumacher — who announced Thursday he will retire at the end of the season — qualified 13th but has a 10-place penalty for causing a crash in the Singapore Grand Prix so will start on the back row.
Sauber driver Kamui Kobayashi gave the local fans a thrill by qualifying fourth, ahead of Lotus' Romain Grosjean.
Sauber's Sergio Perez, who will switch to McLaren next season to replace the Mercedes-bound Hamilton, was sixth while Force India's Nico Hulkenberg was 10th but will drop five places for changing a gearbox in the pre-qualifying practice session.