The opening day of track action at the Suzuka Circuit got underway beneath overcast skies with specks of rain turning into heavy drizzle towards the end of the opening 90 minutes of practice.
Vettel set the pace in that session with a one minute, 29.166 second lap, edging out his Formula One championship rival Lewis Hamilton's Mercedes at the top of the timesheets.
The rain became heavier through the afternoon and was positively lashing the 5.8km circuit by the time the clock ticked down to signal the start of the second 90-minute session.
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The start of the session was delayed by 45 minutes as drains overflowed and rivers of water coursed down inclines at the undulating track.
World championship leader Hamilton went fastest in that session, setting a time of one minute, 48.719 seconds, kicking up a dense mist of spray as he toured the circuit, nearly 20 seconds off Vettel's morning best on a dry track.
The Force India pair of Sergio Perez and Esteban Ocon, and Williams duo Felipe Massa and Lance Stroll were the only other cars brave enough to attempt a flying lap.
The 18-year-old rookie Stroll was briefly caught out by the conditions, running wide and skirting the barriers before rejoining the track without causing damage to his car.
The Canadian's excursion elicited a rare smile from Kimi Raikkonen but neither the Finn nor his team mate Vettel set a time, both completing just a sole installation lap.
Hamilton leads Vettel by 34 points in the overall standings with five of the season's 20 races remaining.
The German suffered successive setbacks at the last two races in Singapore and Malaysia, which Hamilton capitalised on with a win and second-place finish to extend his advantage.

Sebastian Vettel of Germany and Ferrari walks during previews ahead of the Formula One Grand Prix of Japan at Suzuka Circuit

Image credit: Getty Images

Mercedes struggled for speed at both grands prix, though, with the reigning champions only the third fastest team on both occasions, and Friday's rain-hit practice offered few clues as to whether the team had rediscovered its lost pace.
The Red Bull's of Daniel Ricciardo and Max Verstappen, who won the last race in Malaysia, did not set a time in the afternoon but had been third and sixth quickest in the morning session, respectively.
Valtteri Bottas, in the other Mercedes, ended the day fifth with his morning's best as Ocon came seventh.
Nico Hulkenberg was eighth for Renault, ahead of Haas driver Romain Grosjean, while Stoffel Vandoorne set the 10th fastest time in his McLaren at power unit supplier Honda's home race.
The morning session did not pass without incident, however, as Carlos Sainz brought out the red flags after 51 minutes when the Spaniard crashed after losing control of his Toro Rosso at the exit of the turn 11 hairpin.
The Renault-bound Spaniard, already set for a hefty grid penalty for exceeding his power unit component allocation, walked away unscathed but his car came to a rest across the track, leading to a 16-minute delay as the debris was cleared.
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