Kobayashi, who now looks set to stay on in the Japanese series next year after hinting at an exit previously, posted a time of 1m36.296s in his Toyota-powered KCMG SF23 on Thursday afternoon to end the three-day test on top.
The Le Mans 24 Hours lap record holder had an inauspicious start to the day when he crashed at the final corner and brought out an early red flag, but was able to return to the track later and set a time that was seven tenths quicker than the lap with which TOM'S driver Sho Tsuboi had topped the opening day's running.
Nearly all of the fastest times from the test were set in the fourth session on Thursday as the rubber laid in and drivers experimented with low-fuel short runs.
Kobayashi's team-mate Nirei Fukuzumi made it a 1-2 for KCMG at the top of the combined order, lapping the Suzuka circuit in 1m36.337s to end up just 0.059s behind his countryman.
Fukuzumi, who is ending a decade-long relationship with Honda in favour of a move to rival Toyota, is vying for the second seat at the Hong Kong-based squad alongside Impul outcast Yuhi Sekiguchi.
Seven-time Super Formula race winner Sekiguchi drove for KCMG on the opening day and set a time of 1m37.027s in the morning session, which put him second at the end of the day's running but well outside the top 10 in the overall order.
Third place in the combined standings went to Day 1 pacesetter Tsuboi, the newly-crowned SUPER GT champion improving by six tenths on Thursday to set a best time of 1m36.363s.Tsuboi is expected to replace reigning Super Formula champion and his GT500 team-mate Ritomo Miyata at Toyota powerhouse TOM'S next year following the 24-year-old's move to Formula 2 with Rodin Carlin.
Red Bull/Honda junior Ayumu Iwasa ended up fourth in the order, just 0.024s behind Tsuboi, as the top Honda driver in the standings. Being a complete newcomer to Super Formula, Iwasa was able to get three days of track action in the Mugen SF23, including on the final day of running reserved for rookies.
Iwasa's quickest time came on Friday morning, having been unable to set a time in the 1m36s bracket on Thursday afternoon when most of his rivals focused on short runs.
Behind Iwasa, Kenta Yamashita finished a strong fifth for Kondo Racing with a time of 1m36.392s, just edging out Toshiki Oyu in the lead Inging car. Oyu, like Fukuzumi, is leaving Honda after a trying dual campaign in both Super Formula and SUPER GT with the Sakura-based manufacturer.
Sauber Formula 1 junior Theo Pourchaire enjoyed a fruitful first test in Super Formula as he ended up a solid seventh in the timesheets with a best effort of 1m36.586s, just three tenths down on Kobayashi's chart-setting lap.
The French driver was a distant 18th after the first session on Wednesday but was able to improve his times by nearly three seconds to comfortably outshine 2016 champion Yuji Kunimoto in the other Impul car.
Despite being new to Super Formula, Pourchaire did not take part in the final day of running, with Impul instead offering track time to Jota's new Hypercar driver in the World Endurance Championship, Oliver Rasmussen.
The top 10 in the standings was completed by Dandelion duo Kakunoshin Ota and Tadasuke Makino, the two separated by just 0.036s.
Despite only 22 seats being available on the 2024 Super Formula grid across 12 teams, a total of 32 drivers got to drive the series' latest-gen SF23 car in the three-day test at the Japanese Grand Prix venue.
Among the drivers to get their first taste in what is touted as the fastest car outside of F1 was 17-year-old Juju Noda, who posted a best time of 1m38.539s for TGM in her first professional outing in Japan.
Factory Lexus driver Ben Barnicoat took over the #36 TOM'S car previously driven by Ukyo Sasahara on the final day to post a reasonable time of 1m37.482s in the morning session.
Barnicoat was one of the 12 rookies to appear at Suzuka on Friday, a list that also included Super Formula Lights runner David Vidales, Swedish racer Rasmus Lindh and Indy NXT rookie of the year Nolan Siegel.
