The #3 Nissan Z was the car to beat throughout Saturday's running, as Takaboshi paced both free practice and the first segment of qualifying, before Chiyo took over for the Q2 pole shootout.
Chiyo posted a best lap of 1m35.931s to grab the top spot on tyre supplier Michelin's farewell GT500 weekend, which was enough to beat the Real Racing Honda NSX-GT of Nobuharu Matsushita by 0.392 seconds.
The bonus point for pole for Chiyo and Takaboshi closes the gap in the championship to TOM'S Toyota GR Supra pair Sho Tsuboi and Ritomo Miyata to six points.
Tsuboi qualified third, 0.675s off the pace, putting himself and Miyata in a strong position to secure the second position they need to guarantee themselves the title even if Chiyo and Takaboshi win the race.
Two more Nissan crews completed the top five, with Daiki Sasaki putting the Kondo Racing Z fourth ahead of the second of the NISMO-run machines of Ronnie Quintarelli.
Iori Kimura, Naoki Yamamoto's stand-in at the Kunimitsu Honda squad, was sixth-fastest ahead of Takuya Izawa in the Nakajima NSX-GT and Kazuya Oshima in the Rookie Toyota.
There was drama at the end of Q1 as a last-minute flyer from Kakunoshin Ota in the Nakajima Honda pushed the #16 ARTA NSX-GT of Hiroki Otsu down to ninth place, dropping the marque's only title contender out in Q1.
Otsu and Nirei Fukuzumi, who trail Tsuboi and Miyata by 16 points, have to win the race to give Honda any chance of the title in the final race weekend for the NSX-GT.
Cerumo Toyota driver Hiroaki Ishiura could only manage the 12th-fastest time in Q1, meaning team-mate Yuji Tachikawa didn't make an appearance in qualifying in his final race weekend before retirement.
GT300: Pole for Inging keeps title hopes alive
Inging Toyota GR86 GT drivers Hibiki Taira and Yuui Tsutsumi kept their slim hopes of a comeback GT300 title alive by scoring the bonus point for pole position.
Taira and Tsustumi came to Motegi 20 points down in the standings and needing pole to stop their rivals in the Saitama Toyopet Toyota GR Supra, Hiroki Yoshida and Kohta Kawaai, being crowned on Saturday.
But after Taira topped his Q1 group, Tsutsumi did likewise in the Q2 pole shootout, posting a best time of 1m45.633s to beat the JLOC Lamborghini Huracan of Takashi Kogure by 0.152s.
Third-fastest was the LEON Racing Mercedes-AMG GT3 of Naoya Gamou, just a further 0.002s back, followed by the works Subaru BRZ of Hideki Yamauchi and Shun Koide in the UpGarage Honda NSX GT3.
Kawaai could only qualify the Saitama Toyopet Toyota in seventh, but he and Yoshida only need a single point from Sunday's race to wrap up the championship.
