WRT gave Audi its first Intercontinental GT Challenge victory of 2019 following a dominant showing in the second running of the Suzuka 10 Hours.
The #25 crew comprising Kelvin van der Linde, Dries Vanthoor and Frederic Vervisch took the chequered flag 40 seconds clear of the #999 GruppeM Mercedes that won the event last year.
Porsche made it three different manufacturers on the podium, Absolute Racing's #912 911 GT3 R finishing 43s down on the leader in third.
The early stages of the race were dominated by BMW, as the polesitting #42 Schnitzer M6 GT3 led the similar #34 car run by the Walkenhorst team in a one-two.
However, BMW's challenge steadily unravelled, with the #34 Walkenhorst car the first to fall out of contention.
Christian Krognes was running on the tail of the lead BMW when the #5 GTNET Nissan GT-R NISMO GT3 and the #88 JLOC Lamborghini Huracan GT3 came to blows at the Spoon Curve.
While Augusto Farfus was able to navigate his way through the scene, Krognes was unlucky to collect the Nissan, which rolled backwards and into the path of the BMW - the damage to which proved terminal.
Not long after the incident, the Schnitzer BMW was undercut for the lead by the WRT Audi, but the real damage to the German team was done when it copped a drivethrough penalty for failing to respect the minimum pitstop time.
The penalty, handed at the start of the fifth hour, dropped it to fifth, giving Audi a clear path to its first IGTC victory since last year's California 8 Hours.
The WRT crew was able to stretch a 40-second advantage after passing the BMW, and then rebuilt its lead after the field was neutralised in the sixth hour when Nick Cassidy lost the rear of his HubAuto Corsa Ferrari 488 GT3 and shunted heavily at 130R.
Audi was on course for a one-two finish, but the #125 Absolute Racing R8 LMS of Markus Winkelhock, Christopher Mies and Christopher Haase suffered a refuelling issue at the final round of pitstops and dropped to seventh.
That elevated the GruppeM Mercedes of Rafaelle Marciello, Maximilian Buhk and Maro Engel up to second, ahead of Absolute's Porsche entry driven by Dennis Olsen, Matt Campbell and Dirk Werner.
Those two entries enjoyed a long battle for what turned out to be second place, with the order between the two settled only in the eighth hour.
The #77 CraftBamboo Mercedes of Maximilian Gotz, Luca Stolz and Yelmer Buurman finished fourth, with the #42 Schnitzer BMW of Farfus, Nick Yelloly and Martin Tomczyk eventually crossing the line in fifth.
Nissan was the leading Japanese manufacturer thanks to the #35 KCMG GT-R crew of Tsugio Matsuda, Katsumasa Chiyo and Joshua Burdon, which passed the #107 Bentley Continental GT3 late in the race for sixth.
Goodsmile Racing was the highest-classified SUPER GT entry, as Kamui Kobayashi, Nobuteru Taniguchi and Tatsuya Kataoka finishing 10th in the #00 Mercedes-AMG GT3.
Double Formula 1 champion Mika Hakkinen, making his first competitive outing since 2013, finished 22nd in the Planex Smacam McLaren 720s GT3 he shared with Hiroaki Ishiura and Katsuaki Kubota.
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