SARD Toyota man Kovalainen was second-fastest in qualifying, losing out only to TOM'S driver Kenta Yamashita, in the #39 GR Supra he shares with Yuichi Nakayama.
It was the ex-Formula 1 star's best qualifying showing since the final round of the 2016 season, in which he won the title for SARD alongside Kohei Hirate.
Heikki Kovalainen（#39 DENSO KOBELCO SARD GR Supra）
Kovalainen and Nakayama won the previous SUPER GT race at Fuji, which has been the highlight of a mixed campaign that has yielded only another two top-five finishes.
It leaves Nakayama with an outside chance of winning the title, although he goes into the race 10 points down on fellow Toyota man Ryo Hirakawa in the #37 TOM'S car.
"[In the last few seasons] we’ve always won a race when we’ve been low on ballast and everyone else has had a lot of ballast, and it doesn’t feel that good," said Kovalainen, who missed the first two races of the year due to travel restrictions and thus can't win the title.
"You want to perform well in the races when nobody has ballast or restrictors, because it’s the true measure of performance. And I’m happy that we have genuine pace this weekend.
"I enjoyed the race at Motegi, even if it was only for eighth [that we were battling for], and I really hope we can challenge [for the win] tomorrow."
Yamashita asked not to do Q1
Yamashita was Kovalainen's replacement at SARD during the opening round of the season at Fuji in July, and made his first SUPER GT start since then last time out at Motegi as the replacement for Formula E-bound Nick Cassidy alongside Hirakawa at TOM'S.
At Motegi, Yamashita was knocked out in Q1, and he admitted to Motorsport.com that for that reason he asked TOM'S if he could take charge of Q2 instead.
He went on to break the track record established by Honda man Nirei Fukuzumi in qualifying earlier this year, and beat Kovalainen to pole by four tenths.
"To be honest, I was really worried about dropping out in Q1 after Motegi," said Yamashita. "So I asked the team before qualifying if Ryo could do Q1.
"Ryo was the fastest and I was really nervous. But the car felt good. I was surprised by the tyre grip in Q2, and my lap was good."
On his and Hirakawa's race prospects, Yamashita added: "I think I will do the first stint. I’m worried about the tyre warm-up because the temperature will be low, lower than today. But we have a good pace over a stint, so it should be okay after the first couple of laps."
Kenta Yamashita（#37 KeePer TOM’S GR Supra）