Vettel secured his first pole position since the Canadian GP in June with a lap of 1 minute, 27.064 seconds, 0.189 seconds ahead of teammate Charles Leclerc.
"It was not easy, the conditions were very different from Friday and we didn't expect to be on the front row," Vettel said. "What we had was unbelievable, the car felt light and there was a headwind which is what you like."
Mercedes drivers Valtteri Bottas and Lewis Hamilton were third and fourth, respectively, followed by the Red Bulls of Max Verstappen in fifth and Alexander Albon in sixth.
"We seemed quite strong, but we always knew Ferrari might have something in reserve," Bottas said. "In Q3 they looked untouchable."
Organizers canceled Saturday's qualifying session with Typhoon Hagibis set to hit Japan's main island. At least seven people have died while 15 are missing after the massive typhoon lashed a wide area of the country.
Qualifying at Suzuka was also moved to Sunday morning as a result of bad weather in 2004 and 2010.
While the track was dry Sunday morning, lingering winds from the typhoon resulted in several crashes early in the morning session.
The Williams of Robert Kubica crashed into the wall just two minutes into qualifying bringing out the red flag.
Haas driver Kevin Magnussen also crashed early in the session.
Hamilton, who has a commanding 73-point lead over Bottas with five races left, has won here in four of the last five races.
If Hamilton is able to win here, he will equal Michael Schumacher's record for the highest number of wins at the Japanese GP with six. Hamilton won with McLaren in 2007 and with Mercedes in 2014, 2015, 2017 and last year.
Vettel has also had success here, winning four times between 2009 and 2013.
McLaren driver Carlos Sainz Jr. was seventh followed by teammate Lando Norris. Toro Rosso's Pierre Gasly was ninth while Haas driver Romain Grosjean rounded out the top ten.