From second on the grid, Baguette laid the foundations for victory by passing the polesitting Cerumo Toyota of Yuji Tachikawa on lap eight of 63.
From there, he and Tsukakoshi survived two safety car restarts in the #17 Honda NSX-GT, overcoming their 46kg success handicap to take victory over the Cerumo car shared by Tachikawa and Ishiura by a comfortable 7.796s seconds.
It means Baguette and Tsukakoshi move into a one-point lead in the championship ahead of the TOM'S Toyota drivers Yuhi Sekiguchi and Sacha Fenestraz.
Poleman Tachikawa led the opening laps in the #38 Toyota GR Supra but was unable to shake off Baguette and the #64 Nakajima Honda of Takuya Izawa, who formed a breakaway trio.
Baguette's opportunity to pass Tachikawa came when the pair encountered GT300 traffic at the hairpin, with the Belgian driver moving to the outside and then forcing his rival across the track on the exit to snatch the position.
Just two laps later the safety car was called for the first time as the #87 JLOC Lamborghini Huracan spun after apparent contact with the #8 ARTA Honda and crashed into the #19 Bandoh Toyota, which had been running a strong fifth, at Turn 9.
When action resumed on lap 15, Baguette built up an advantage over Tachikawa, as Izawa began to come under pressure from the chasing pack.
Baguette surrendered the lead on lap 25 when he pitted to hand over to Tsukakoshi, with Tachikawa coming in to give the Cerumo car to Hiroaki Ishiura two laps later.
Ishiura narrowly came out ahead but on cold tyres he was powerless to hold off Tsukakoshi, who quickly pulled out a gap and was almost 10s to the good when the safety car was called for a second time on lap 46 for debris.
That debris was the result of the two TOM'S Toyotas of Sekiguchi and Nick Cassidy making contact at Turn 11 as Cassidy attempted to pass up the inside.
The race resumed on lap 51, and Tsukakoshi was never seriously threatened on his way to the chequered flag, as Ishiura pocketed a first podium of 2020 for the #38 car in second.
Third went to the #16 Mugen Honda of Hideki Mutoh and Ukyo Sasahara in by far the best showing of the season so far for a Yokohama-shod car.
More to follow