Kobayashi took the top spot with a best time of 1m27.794s around halfway through the 15-minute Hypercar qualifying session on Saturday afternoon, scoring a crucial bonus point for himself and his team-mates Jose Maria Lopez and Mike Conway.
Brendon Hartley was 0.624 seconds adrift of Kobayashi in the #8 Toyota, ahead of the two factory Penske-run Porsche 963s.
Kevin Estre briefly topped the times at the wheel of the #6 Porsche before both Toyotas set their fastest times of a session that took place on a virtually dry track, but with some damp patches from earlier rain.
The French driver’s effort of 1m28.687s was still enough for third ahead of team-mate Frederic Makowiecki in the sister #5 car.
Next up was the solo Cadillac V-Series.R driven by Alex Lynn, who was the last driver to get within a second of the pace of Kobayashi.
Ferrari suffered a subdued qualifying session as its pair of 499Ps could only manage sixth and seventh places, marking the first time this season it hasn’t got one of its cars in the top three.
James Calado set the Italian marque’s best time of 1’28.991s, almost 1.2s off the pace, in the #51 car, while Nicklas Nielsen was fractionally slower in the #50 Ferrari.
Next up was the JOTA customer Porsche of Antonio Felix da Costa in eighth, followed by the Proton example of Neel Jani and the two Peugeot 9X8s, which struggled badly for pace in 10th and 11th places with Mikkel Jensen and Loic Duval at the wheel.
The solo Vanwall Vandervell 680 propped up the order in Hypercar with Tristan Vautier driving.
United Autosports topped LMP2 qualifying courtesy of Philip Hanson, who took the #22 ORECA 07’s first pole of the year and a third in total for the team.
Hanson posted a best time of 1m32.182s in the car he shares with Filipe Albuquerque and Frederick Lubin, which was just 0.091s clear of nearest rival Louis Deletraz in the #41 WRT ORECA.
Oliver Jarvis ensured both United cars will start in the top three ahead of the JOTA machine of Pietro Fittipaldi and the Le Mans class-winning Inter Europol Competition car of Albert Costa.
Vector Sport’s Gabriel Aubry suffered a lurid lock-up at Turn 1 just after setting his fastest time, which in the end was only enough for sixth.
In GTE Am, Ben Keating delivered Corvette Racing, which has already clinched this year’s title, a third pole of the season.
Keating, who shares the solo Corvette C8.R with Nicky Catsburg and Nico Varrone, bested his usual rival Sarah Bovy in the Iron Dames Porsche by a scant 0.035s on what was still a damp track.
Satoshi Hoshino put the D’station Racing Aston Martin third ahead of the Heart of Racing example driven by Ian James, while leading the Ferrari contingent was Hiroshi Koizumi in the #21 AF Corse car.
The WEC 6 Hours of Fuji is scheduled to begin at 11am local time (GMT +9) on Sunday.