[1] Team Mach returned to the championship at Suzuka, however they had swapped their Ferrari 458 Italia GT3 they started the season with, replacing it with a Nissan GT-R GT3.
Gran Turismo Academy winner Lucas Ordóñez was entered in the race with NDDP Racing while former World Touring Car Championship and American Le Mans Series driver Jörg Müller was entered as a third driver for the GSR Hatsune Miku team.
As in the 2012 race, 2013 All-Japan Formula Three champion Yuichi Nakayama was the third driver for apr, while Carlo van Dam returned to Super GT with the Cars Tokai Dream28 McLaren.
The teams ranked 1st, 3rd, 5th and 6th in the GT300 championship prior to Suzuka weren't fast enough to qualify for the second session.
The #87 JLOC Lamborghini Gallardo GT3 with Hiroki Yoshimoto driving had technical trouble and only ran one lap and was off the pace.
In the second GT300 qualifying session for the thirteen fastest cars in the first qualifying session, Kota Sasaki wasn't able to beat his teammate's Q1 time but was still able to get their fourth pole position of the 2013 season with a 2:01.693, 0.782 seconds faster than Daiki Sasaki in the #3 NDDP Racing Nissan GT-R GT3.
The #61 Subaru BRZ led from pole position and was able to consistently lap faster than the field, after one-third race distance Sasaki and Takuto Iguchi who drove the 2nd stint in the car was 90 seconds ahead of the #4 GSR Hatsune Miku BMW.
the #36 Lexus Team Petronas TOM'S entry of Kazuki Nakajima and James Rossiter finished in 3rd place after João Paulo de Oliveira ran off course with 3 laps to go and dropped the #12 Calsonic Team Impul Nissan GT-R to 4th.
[5] The #4 GSR Hatsune Miku BMW that finished 2nd in the GT300 class was later disqualified after it failed post-race inspections.