KCMG Toyota driver Kobayashi set the best time of the day at the end of the two-hour afternoon session amid a flurry of lap times set on new tyres, heading the order with a 1m36.183s effort.
That was a tenth faster than he managed on the opening day of the test, but a little over two tenths shy of the benchmark established by Nojiri on Monday.
After topping the first day of running, Nojiri's afternoon session was interrupted by a crash at Turn 6 that brought out the red flags. His Team Mugen machine appeared to suffer little damage in the impact, and he was able to rejoin the track for the closing 15 minutes.
Nonetheless, the two-time champion did not improve his best time, with his fastest lap from the morning session leaving him 16th and over a second off the pace set by Kobayashi.
Toshiki Oyu was second-fastest for the rebranded TGM Grand Prix squad, albeit 0.385s behind Kobayashi, while Ryo Hirakawa - celebrating his 29th birthday on Tuesday - was third for Team Impul.
Red Bull junior driver Liam Lawson was an encouraging fifth-fastest and within half a second of the pace in his Team Mugen machine, just behind the TOM'S car of Ritomo Miyata.
The morning session was topped by a surprise face in the form of Rookie Racing's Kazuya Oshima, who failed to score a single point last season. His best time of 1m36.817s left him seventh overall behind Dandelion Racing's Tadasuke Makino.
Naoki Yamamoto was second-fastest in the morning for Nakajima Racing and ninth overall behind Dandelion substitute driver Hiroki Otsu, followed by Yuji Kunimoto in the second of the KCMG cars.
Of the other rookies, Raoul Hyman was 20th for B-Max Racing, albeit much closer to the pace than he had been on Monday, while Cem Bolukbasi was three seconds off the pace in 21st after appearing to suffer a problem with his TGM Grand Prix car in the morning.
Besides Nojiri, the only other driver to cause a red flag was Nakajima Racing's Ren Sato, who went off at Turn 7 (formerly Dunlop corner) late in the morning session. The damage was sufficient to leave him out of action for the rest of the day.
In between the two Super Formula sessions, Super Formula Lights held its first official test session of the year. TOM'S driver Seita Nonaka led team-mate Hibiki Taira, while Enzo Trulli was best of the international drivers in fifth.
Two more Lights sessions take place on Wednesday, but for the Super Formula field the next track action will be free practice for the opening round at Fuji Speedway on April 7-9.
Suzuka testing times:
| Pos. | No. | Driver | Team/Engine | Morning | Afternoon |
|---|---|---|---|---|---|
| 1 | 7 |
 Kamui Kobayashi |
KCMG/Toyota | 1'38.219 | 1'36.183 |
| 2 | 53 |
Toshiki Oyu |
TGM/Honda | 1'37.412 | 1'36.568 |
| 3 | 20 |
Ryo Hirakawa |
Impul/Toyota | 1'37.969 | 1'36.632 |
| 4 | 37 |
Ritomo Miyata |
TOM'S/Toyota | 1'37.405 | 1'36.642 |
| 5 | 15 |
 Liam Lawson |
Mugen/Honda | 1'37.561 | 1'36.663 |
| 6 | 5 |
Tadasuke Makino |
Dandelion/Honda | 1'37.854 | 1'36.735 |
| 7 | 14 |
Kazuya Oshima |
Rookie/Toyota | 1'36.817 | 1'37.122 |
| 8 | 6 |
Hiroki Otsu |
Dandelion/Honda | 1'37.656 | 1'36.887 |
| 9 | 64 |
Naoki Yamamoto |
Nakajima/Honda | 1'37.037 | 1'40.501 |
| 10 | 4 |
Kazuto Kotaka |
Kondo/Toyota | 1'38.921 | 1'37.048 |
| 11 | 3 |
Ukyo Sasahara |
Kondo/Toyota | 1'37.482 | 1'37.115 |
| 12 | 18 |
Yuji Kunimoto |
KCMG/Toyota | 1'37.185 | 1'37.983 |
| 13 | 39 |
Sena Sakaguchi |
Inging/Toyota | 1'37.374 | 1'37.208 |
| 14 | 38 |
Sho Tsuboi |
Inging/Toyota | 1'37.230 | 1'37.211 |
| 15 | 65 |
Ren Sato |
Nakajima/Honda | 1'37.259 | no time |
| 16 | 1 |
Tomoki Nojiri |
Mugen/Honda | 1'37.330 | 1'40.335 |
| 17 | 36 |
 Giuliano Alesi |
TOM'S/Toyota | 1'37.869 | 1'37.371 |
| 18 | 50 |
Nobuharu Matsushita |
B-Max/Honda | 1'37.524 | 1'37.432 |
| 19 | 19 |
Yuhi Sekiguchi |
Impul/Toyota | 1'37.488 | 1'37.582 |
| 20 | 51 |
 Raoul Hyman |
B-Max/Honda | 1'39.858 | 1'37.535 |
| 21 | 55 |
 Cem Bolukbasi |
TGM/Honda | 1'39.408 | 1'39.232 |
| 22 | 12 |
Nirei Fukuzumi |
ThreeBond/Honda | 1'38.846 | 1'39.330 |
