The 60-minute Saturday morning session continued the trend of the quickest times being set at the start of the session, as Nakajima posted a 1m24.078s in the early stages to go quickest.

That was just 0.004s shy of the best time set by Mark Webber's #1 Porsche 919 Hybrid on Friday, and gave the Japanese manufacturer a buffer of 0.422s over nearest rival Audi.

Di Grassi posted a time of 1m24.500s in the #8 R18 e-tron quattro to edge out the best of the Porsches, the #2 driven by Neel Jani, whose effort of 1m24.558s made it three different manufacturers in the top three.

The #6 Toyota TS050 Hybrid of Kamui Kobayashi was fourth fastest, eight tenths down on the pacesetting sister #5 car, followed by the #7 Audi driven by Andre Lotterer and the #1 Porsche of Timo Bernhard.

Rebellion once again had the measure of ByKolles in the privateer LMP1 subcategory, although the #13 car still languished nearly five seconds behind the quickest of the hybrid cars.

G-Drive and Ford lead classes

In LMP2, Will Stevens set the quickest time in the #26 G-Drive Oreca, a 1m21.474s, to go six tenths clear of GP2 regular Antonio Giovinazzi in the #31 ESM Ligier.

Third fastest was the #42 Strakka Gibson with Jonny Kane at the wheel, followed by Pipo Derani in the #30 ESM car.

Ricardo Gonzalez provided some early drama with a spin at Turn 5 in the #43 RGR Sport Ligier, but escaped suffering any damage, the car recovering to go sixth quickest in class.

Topping the GTE-Pro division was Andy Priaulx in the #67 Ford GT, the Guernseyman putting in a lap of 1m38.092s to continue the American marque's strong run so far at Fuji.

Ford's closest challenger came in the form of the #95 Aston Martin of Marco Sorensen, who was four tenths behind Priaulx, while Stefan Mucke made it two Fords in the top three with an identical time (1m38.500s) to the Danish driver.

Ferrari's top representative was the #71 car of Sam Bird, which was fourth fastest.

Aston Martin meanwhile topped the GTE-Am category, with Pedro Lamy setting a best time of 1m39.942s in the #98 car.

Third practice results:

Cla	#	Drivers	Car	Class	Time	Gap
1	5	Anthony Davidson Kazuki Nakajima Sébastien Buemi	Toyota TS050 Hybrid	LMP1	1'24.078
2	8	Lucas di Grassi Loic Duval Oliver Jarvis	Audi R18	LMP1	1'24.500	0.422
3	2	Romain Dumas Neel Jani Marc Lieb	Porsche 919 Hybrid	LMP1	1'24.558	0.480
4	6	Stéphane Sarrazin Kamui Kobayashi Mike Conway	Toyota TS050 Hybrid	LMP1	1'24.895	0.817
5	7	Andre Lotterer Marcel Fassler Benoit Tréluyer	Audi R18	LMP1	1'25.313	1.235
6	1	Mark Webber Timo Bernhard Brendon Hartley	Porsche 919 Hybrid	LMP1	1'25.623	1.545
7	13	Alexandre Imperatori Dominik Kraihamer Matheo Tuscher	Rebellion R-One	LMP1	1'28.881	4.803
8	4	Simon Trummer Oliver Webb Pierre Kaffer	CLM P1/01	LMP1	1'30.865	6.787
9	26	Will Stevens Roman Rusinov Alex Brundle	Oreca 05	LMP2	1'31.474	7.396
10	30	Giedo van der Garde Sean Gelael Antonio Giovinazzi	Ligier JS P2	LMP2	1'32.004	7.926
11	42	Jonny Kane Lewis Williamson	Gibson 015S	LMP2	1'32.196	8.118
12	31	Pipo Derani Ryan Dalziel Chris Cumming	Ligier JS P2	LMP2	1'32.201	8.123
13	36	Nicolas Lapierre Gustavo Menezes Stéphane Richelmi	Alpine A460	LMP2	1'32.369	8.291
14	43	Bruno Senna Ricardo Gonzalez Filipe Albuquerque	Ligier JS P2	LMP2	1'32.437	8.359
15	35	Paul-Loup Chatin Ho-Pin Tung David Cheng	Alpine A460	LMP2	1'32.474	8.396
16	45	Shinji Nakano Tor Graves Alex Lynn	Oreca 05	LMP2	1'32.740	8.662
17	37	Vitaly Petrov Viktor Shaytar Kirill Ladygin	BR01	LMP2	1'32.778	8.700
18	27	Maurizio Mediani Nicolas Minassian Mikhail Aleshin	BR01	LMP2	1'33.160	9.082
19	44	Roberto Merhi Richard Bradley Matthew Rao	Oreca 05	LMP2	1'33.292	9.214
20	67	Harry Tincknell Andy Priaulx	Ford GT	LMGTE PRO	1'38.092	14.014
21	95	Marco Sorensen Nicki Thiim	Aston Martin Vantage V8	LMGTE PRO	1'38.500	14.422
22	66	Stefan Mücke Olivier Pla	Ford GT	LMGTE PRO	1'38.500	14.422
23	71	Sam Bird Davide Rigon	Ferrari 488 GTE	LMGTE PRO	1'38.859	14.781
24	97	Darren Turner Richie Stanaway	Aston Martin Vantage V8	LMGTE PRO	1'38.889	14.811
25	77	Richard Lietz Michael Christensen	Porsche 911 RSR (2016)	LMGTE PRO	1'39.141	15.063
26	51	Gianmaria Bruni James Calado	Ferrari 488 GTE	LMGTE PRO	1'39.358	15.280
27	98	Pedro Lamy Paul Dalla Lana Mathias Lauda	Aston Martin Vantage V8	LMGTE AM	1'39.492	15.414
28	86	Michael Wainwright Adam Carroll Ben Barker	Porsche 911 RSR	LMGTE AM	1'40.092	16.014
29	83	François Perrodo Emmanuel Collard Rui Aguas	Ferrari F458 Italia	LMGTE AM	1'40.428	16.350
30	78	Christian Ried Wolf Henzler Joel Camathias	Porsche 911 RSR	LMGTE AM	1'40.668	16.590
31	88	David Heinemeier Hansson Patrick Long Khaled Al Qubaisi	Porsche 911 RSR	LMGTE AM	1'40.964	16.886
32	50	Pierre Ragues Ricky Taylor Yutaka Yamagishi	Chevrolet Corvette C7-Z06	LMGTE AM	1'41.693	17.615