With rain forecast for the afternoon, teams wasted no time getting up to speed - leading to several changes at the top as Ferrari, Mercedes and Red Bull once again proved incredibly evenly matched.
Vettel eventually settled matters in the Scuderia's favour with a late flyer of 1m 29.166s on Pirelli's supersoft tyres - just over two-tenths quicker than Hamilton's best. Ricciardo and Kimi Raikkonen were fractions further down the road, meaning the top four drivers - comprising three teams - were all covered by less than half a second.
Vettel's best time came shortly after Sainz violently hit the barriers exiting the Turn 11 hairpin. The Spaniard inadvertently dropped a rear wheel on the dirt exiting the left-hander, flicking his Toro Rosso sideways and sending it spearing into the inside tyre wall. Sainz, who carries a 20-place grid penalty into Sunday's race, was unhurt, although his car suffered extensive damage.
At that point it was Hamilton who had set the pace, a few hundredths ahead of Vettel - but with the latter yet to complete a run on the supersoft. When the session resumed Ferrari duly sent out both their drivers on the red-marked compound, with Vettel surging ahead - his time eclipsing the official lap record, and coming close to the quickest ever lap of Suzuka, dating back to Michael Schumacher and 2006.
A late spell of rain ensured Vettel's time went unchallenged over the final five minutes.
Valtteri Bottas finished fifth in the second Mercedes, albeit almost a second back from Vettel - while Max Verstappen paid the price for a wild moment at Spoon that consigned him to sixth in the second Red Bull. The Dutchman also experienced charging issues on a subsequent attempt to improve.
Esteban Ocon led the rest of the pack in seventh, with the Force India man leading a tight chain of cars comprising Renault's Nico Hulkenberg, Haas's Romain Grosjean and McLaren's Stoffel Vandoorne.
Kevin Magnussen backed up a strong showing for Haas by edging McLaren's Fernando Alonso for 11th, despite being kept in the garage for much of the opening half of the session by a water pressure issue.
Sainz eventually wound up 17th, one spot and a few tenths ahead of Toro Rosso team mate Pierre Gasly.
WATCH: FP1 Summary
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