The German, who trails Mercedes rival Lewis Hamilton by 34 points with five races left this season, steered his Ferrari to a fastest lap of one minute, 29.166 seconds in light drizzle at Suzuka.
Hamilton clocked the next quickest time, 0.2 seconds behind Vettel in dry conditions, before Carlos Sainz rammed into a wall and brought a temporary halt to proceedings with half an hour left.
Australian Daniel Ricciardo roared to a 1:29.541 lap after bolting on the super-soft tires, while Ferrari’s Kimi Raikkonen was the only other driver to break 1:30 despite complaining of overheating brakes.
Vettel’s time came after the removal of Sainz’s battered vehicle, the four-time world champion pointing his finger angrily at Sauber’s Marcus Ericsson as he crossed the line.
Valtteri Bottas registered a 1:30.151 for Mercedes with Red Bull’s Max Verstappen – who ambushed Hamilton to win in Malaysia last weekend – sixth fastest.
Vettel, who finished fourth in Sepang after starting from the back of the grid, faces a must-win race at the fearsome figure-of-eight Japanese circuit, where he won four times with Red Bull.
Verstappen had a fright as he slid off onto the gravel before Sainz smashed into a tire wall after exiting the hairpin, mangling his Toro Rosso and bringing out the red flags.
“I don’t know what happened. I lost the car,” said the Spaniard over the radio before climbing out of the wreckage unhurt.
Esteban Ocon’s Force India and Nico Hulkenberg in a Renault were seventh and eighth quickest, while Romain Grosjean’s Haas and the McLaren of Stoffel Vandoorne rounded out the top 10.
Rain has also been forecast for the afternoon’s second free practice.