Antonio Fuoco set a best time of 1m35.649s at the end of the 90-minute session in the #50 Ferrari 499P LMH, a massive 2.6 seconds up on the sister #51 machine as the track rapidly improved late on.
Best of the rest in third was the #94 Peugeot 9X8, followed by the two works Penske Porsche 963s in fourth and fifth, while home favourite Toyota was sixth and seventh with its two GR010 HYBRIDs.
Despite the looming threat of Typhoon Yun-yeung, Friday morning's 90-minute session started on schedule at 11am local time in wet conditions and passed largely without incident.
Almost every Hypercar class manufacturer enjoyed a stint at the top of the times, as the track steadily dried out.
Ferrari took command of the times with a little over 30 minutes to go as James Calado went quickest in the #51 car, with team-mate Antonio Giovinazzi becoming the first driver to breach the 1m40s mark when he set a 1m39.198s with 22 minutes left on the clock.
Fuoco then traded the top time with Giovinazzi as he took over at the wheel of the #50 Ferrari, with Porsche man Michael Christensen briefly snatching the advantage before Fuoco went faster again, posting a 1m37.616s and then a 1m35.649s after switching to slick tyres.
Giovinazzi set the best time in the #51 car of 1m38.258s on wets, just over four tenths up on late improver Gustavo Menezes in the #94 Peugeot.
Christensen's time was eclipsed late on by his opposite number in the sister #6 Porsche, Laurens Vanthoor, who posted a 1m38.729s to go fourth-fastest.
Mike Conway set the best time for Toyota of 1m39.251s in the #7 car, four hundredths quicker than Brendon Hartley in the #8 car in a subdued opening session for the Japanese manufacturer.
Completing the top 10 were the second of the Peugeots, the #93 car in which Paul di Resta set the best time, the solo Cadillac V-Series.R of Alex Lynn and the Proton Competition customer Porsche of Harry Tincknell.
The JOTA Porsche enjoyed a lengthy spell at the top of the times in the opening half of the session when conditions were at their worst, but ended up 11th in the Hypercar class and slower than the team's LMP2 car, which topped that class.
Oliver Rasmussen put in a late flyer of 1m40.781s aboard the #28 ORECA 07 to take the top spot in LMP2, almost two seconds up on nearest rival Filip Ugran in the #9 Prema machine.
United Autosports was third in class courtesy of a late effort from Ben Hanley - standing in for Tom Blomqvist this weekend - in the #23 entry.
Topping the times by an even wider margin in GTE Am was the #77 Dempsey Proton Porsche 911 RSR-19 of Mikkel Pedersen on a 1m43.538s.
That was almost four seconds up on Davide Rigon, who went second-fastest in the #54 AF Corse Ferrari 488 GTE.
A sole full-course yellow was called at the one-hour mark, but this was purely procedural rather than in response to any accident.
FP2 is scheduled to begin at 3.30pm local time, but more rain is forecast for later in the day, casting doubt on whether the session will run as planned.
Fuji WEC - First practice results:
Alessandro Pier Guidi
Jose Maria Lopez
|Toyota GR010 - Hybrid||HYPERCAR||1'39.251||3.602|
|Toyota GR010 - Hybrid||HYPERCAR||1'39.291||3.642|
Paul di Resta
David Heinemeier Hansson
Antonio Felix da Costa
Joao Paulo de Oliveira
|Vanwall Vandervell 680||HYPERCAR||1'41.483||5.834|
Juan Manuel Correa
|Porsche 911 RSR - 19||LMGTE AM||1'43.538||7.889|
|Ferrari 488 GTE EVO||LMGTE AM||1'47.198||11.549|
|Porsche 911 RSR - 19||LMGTE AM||1'47.230||11.581|
Luis Perez Companc
|Ferrari 488 GTE EVO||LMGTE AM||1'47.250||11.601|
|Aston Martin Vantage AMR||LMGTE AM||1'47.493||11.844|
|Aston Martin Vantage AMR||LMGTE AM||1'47.913||12.264|
|Ferrari 488 GTE EVO||LMGTE AM||1'48.414||12.765|
|Porsche 911 RSR - 19||LMGTE AM||1'49.060||13.411|
|Porsche 911 RSR - 19||LMGTE AM||1'49.199||13.550|
|Porsche 911 RSR - 19||LMGTE AM||1'49.455||13.806|
|Ferrari 488 GTE EVO||LMGTE AM||1'49.706||14.057|
|Chevrolet Corvette C8.R||LMGTE AM||1'50.043||14.394|
Ahmad Al Harthy
|Aston Martin Vantage AMR||LMGTE AM||1'53.388||17.739|