The Ferrari driver qualified third-fastest at Suzuka, but will start on the front row thanks to a gearbox penalty for Bottas.
Vettel was second after the first runs, but a small improvement at the end was not enough to stay second.
"In the last run in Q3 I tried a bit more than there was," Vettel explained.
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"Valtteri wasn't a threat, so I took a bit more risk, but it didn't work.
"Still, I am happy with third and the front row tomorrow, the starts lately have been quite good.
"The car balance is getting better and better.
"We are lacking a bit of performance but the car should be a bit better in the race."
Vettel qualified more than four tenths slower than poleman Lewis Hamilton, who he trails by 34 points in the championship.
After a qualifying problem forced Vettel into a charge from the back of the grid in Malaysia last week, with Mercedes vulnerable, Vettel conceded his rival was "back to normal" in Japan.
"I don't know which sort of pace they will have," he said.

Lewis Hamilton.

Image credit: Eurosport

They are a bit up and down, last week they weren't very quick, this race back to normal. For us normally we are a bit stronger in the race compared to qualifying, so we get together and see what we can do at the start and during the race.
Ferrari team-mate Kimi Raikkonen made an error on his first Q3 lap and his second attempt was only good enough for sixth.
He will drop further down the grid thanks to a gearbox penalty earned from a crash in FP3, and Vettel said it was "not ideal" but stopped short of suggesting it was hurting his own chances not having his team-mate closer to support him.
"There was a small issue that led to a problem with Kimi's car," said Vettel.
"The car is quick, last weekend showed that if you start out of position, you can still get back.
"I am sure he can have a strong race from where he starts."
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