Jenson Button and Naoki Yamamoto's Super GT title defence got off to a bad start with their car being hit by another Honda while leading the rain-truncated Okayama opener.
Nissan had dominated Saturday's qualifying with a new lap record, but the wet conditions that prevailed on Sunday played into the hands of the Honda runners.
Yamamoto took the driving duties in the #1 Kunimitsu Honda NSX-GT for the first stint, starting just behind the NISMO and Impul Nissans that locked out the front row.
The safety car led the field at the start of the race due to heavy rain showers, but the conditions were suitable enough for racing to begin on lap four.
Yamamoto was immediately on the move, seizing second position from Impul Nissan driver Daiki Sasaki at Turn 1.
Soon afterwards, the safety car had to be deployed again when a Toyota GT300 car spun at Turn 1, taking another car along with it. A long intervention followed before racing resumed on lap 10.
Once again, Yamamoto was on the charge at the restart, passing the polesitting NISMO Nissan of Ronnie Quintarelli around the outside of Turn 1 to grab the lead.
Behind, Koudai Tsukakoshi of Real Racing also starting moving towards the front of the pack, overtaking both the Impul and NISMO GT-Rs to establish an early 1-2 for Honda.
Just as the Hondas started extending their advantage at the front, several GT300 cars crashed at the Moss S corner as the rain intensified - bringing out the red flags.
The race was halted for over 45 minutes and resumed behind the safety car, with the race finally recommencing lap 20.
When the action commenced, Tsukakoshi attempted to pass Yamamoto on the outside of Turn 1 only to clatter into the Kunimitsu driver and leave him beached in the gravel.
Tsukakoshi was able to hold onto the lead despite the contact, while a safety car had to be called in to retrieve the stricken car of the reigning champion.
With the help of the marshals, Yamamoto's car was pushed out of the gravel and he was able to rejoin the race a lap down.
But with conditions worsening, the safety car remained on track for several more laps, until the race was stopped again.
A decision to not restart the race was taken soon after, with the results declared on lap 31 and half-points awarded.
Tsukakoshi and Bertrand Baguette's Real Racing entry was handed a penalty for the incident with the Kunimitsu Honda, dropping them to second-to-last.
That meant ARTA pair Izawa and Tomoki Nojiri were declared the winners, having early passed the NISMO entry of Quintarelli and Tsugio Matsuda.
The podium was completed by the Impul Nissan team of Sasaki and James Rossiter.
Yamamoto and Button finished a lap down and last of the classified finishers in 15th.