The German, who trails championship-leading Mercedes rival Lewis Hamilton by 34 points in the overall standings with five races left, could only manage the third-fastest time as the Briton smashed the track record at the Suzuka circuit to seize a dominant pole.
Vettel’s best was nearly half a second slower than the triple champion’s benchmark time.
Although he is set to start alongside his rival on the front row in second, thanks to a five-place grid penalty for Valtteri Bottas, the Mercedes driver’s speed could prove too much to overcome. “I don’t know which sort of pace they will have,” said the four-times champion, trying to put a positive spin on the situation, but cutting a subdued figure.
“Obviously, you always know what you are doing but they have been a bit up and down: last week they weren’t very quick.
“This weekend they seem to be back to normal…”
Ferrari were ominously fast as Mercedes struggled in the sweltering heat of the last two races in Singapore and Malaysia.
But the Maranello-based team’s challenge imploded.
Vettel and Kimi Raikkonen crashed out on the opening lap in Singapore.
Engine issues forced the German to line up last in Malaysia and prevented his Finnish team mate from even making the start.
Hamilton capitalised on his rival’s misfortune, winning at the floodlit Marina Bay track and finishing second in Sepang.
Vettel, encouraged by Ferrari’s pace, arrived in Japan hopeful of narrowing the gap to Hamilton but Mercedes appear to have regained the edge in Suzuka’s cooler conditions.
Temperatures are expected to be warmer on Sunday, however, and Vettel’s hopes now rest on conditions hotting up enough to handicap Mercedes.
“I think there should be sunshine which makes everything a bit hotter, so let’s see how that goes,” said Vettel who has conceded 41 points to Hamilton in the last three races and is running out of time to make up the lost ground.
“For us, I think normally we are a bit stronger in the race compared to qualifying, so that’s where I guess we get together and see what we can do, at the start and then during the race.”
(Editing by Ed Osmond)
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