Practice began on a wet track following a brief shower earlier on Saturday morning, but conditions improved sufficiently for slick tyres to be fitted just 15 minutes into the session.
Ferrari was one of the first teams to make the move away from wets, with Alessandro Pier Guidi immediately improving by over two seconds to 1m35.275s to go fastest in the #51 499P.
Lap times continued to tumble as the track improved further, with the leading drivers dipping into the 1m30s window just after the halfway point of the session.
Alex Lynn was the first driver to break the 1m31s barrier, lapping the former Japanese Grand Prix venue in 1m30.915s in the solo Cadillac V-Series.R.
Brendon Hartley then went three tenths faster in the #8 Toyota, before Yifei Ye found another big chunk of time to move JOTA Porsche 963 to the top.
Ye’s time of 1m30.798s would remain quickest until the final 10 minutes of practice, when Kobayashi got down to a 1m30.068s to put Toyota back ahead.
That time wouldn’t be usurped until the end of the session, putting Toyota on the front foot ahead of qualifying for its home event.
The closest anyone got to Kobayashi’s benchmark was Loic Duval, who clocked a time of 1m30.476s in the #94 Peugeot 9X8 after a comparatively difficult Friday for the French manufacturer.
Antonio Felix da Costa improved on team-mate Ye’s time by nearly three tenths to put the JOTA Porsche third at the finish, just ahead of the second Peugeot of Mikkel Jensen.
JOTA's fellow customer Porsche squad Proton Competition also outpaced the factory 963s despite starting the weekend with an entirely new chassis that only completed 10 laps in a shakedown prior to Fuji, with Harry Tincknell setting the car’s best time of 1m30.710s to end up fifth.
James Calado was sixth in the best of the two factory Ferraris, the #51 car that sits equal-second in the championship, after team-mate Antonio Giovinazzi survived a scary moment when he nearly went into the back of the JOTA Porsche under braking just after halfway through the session.
The championship-leading #8 Toyota was only seventh-quickest in the hands of Ryo Hirakawa, with Cadillac eventually ending up eighth with Lynn’s previous time of 1m30.914s.
The two factory Porsche cars completed the top 10, both ending up more than a second off the pace of the chart-topping Toyota, with the #50 Ferrari and the Vanwall completing the Hypercar field.
In LMP2, Oliver Jarvis set the pace for United Autosports with a best time of 1m34.258s in the #23 ORECA 07, beating the #36 Alpine of Matthieu Vaxiviere by just over two tenths of a second.
The #22 United car was third-quickest with Phil Hanson, while Vector Sport enjoyed a strong showing with Gabriel Aubry taking the team up to fourth with a time of 1m34.719s.
The GTE Am field was led by the #54 AF Corse Ferrari 488 GTE of Davide Rigon, who moved to the top late on with a time of 1m39.074s.
That was after Rigon’s team-mate Francesco Castellacci suffered a puncture in an incident with the Inter Europol LMP2 car of Fabio Scherer at Turn 1 that forced the Le Mans-winning LMP2 team into making a rear wing change.
Second in the GTE Am class was the #777 D’station Aston Martin Vantage GT3 of Tomonobu Fujii, while Mikkel Pedersen made it three different manufacturers inside the top three in the #77 Dempsey-Proton Porsche 911 RSR-19.
Results to follow
