The Team Impul driver qualified seventh for Sunday's race and ran in that position in the early stages until being handed a 10-second stop-and-go penalty for a violation of the start procedure.
By contrast, Nojiri won the race from pole in a repeat of the second leg of last year's Fuji opener to give himself an early championship lead.
Explaining the draconian punishment post-race, Hirakawa revealed it related to an illegal push-back on the grid, a legacy of a software problem that prevented him from participating in warm-up.
"We had an issue with the computer software and we couldn’t run in the eight-minute warm-up as we had to change the software," Hirakawa told Motorsport.com.
"We managed to sort out the issue and we got out, but the bite point of the clutch changed a lot and we wanted to check it on the grid, so we asked someone [an official] on the grid if it was possible, so we did it.
"But then they decided it was illegal. It was just a misunderstanding. When I got the penalty, I was lost for words."
Hirakawa opted to stay out on track when every other car in the field pitted on lap 10 behind the safety car, putting him in the lead of the race, staying out until 39 of 41 before finally coming in for his mandatory tyre change.
But a loose wheel forced him to pull off the track, ending any faint hopes he had of scoring points.
"I think that summed up today," sighed Hirakawa. "The only positive thing was the race pace. I could keep the position and make a gap to Nojiri, although he was able to manage his pace.
"Today’s loss was huge for the championship. I don’t think I could have won, but [without the issues] we could have been on the podium, or at least P5."
With 11 points on the board thanks to his third-place finish in Saturday's opener, Hirakawa is trailing Nojiri by 30 with seven races remaining.
The Toyota driver - who now heads to Portimao to continue his World Endurance Championship campaign next weekend - concedes that Impul is still far away from being able to properly take the fight to the Mugen driver.
"The gap to Nojiri is still too big," admitted Hirakawa. "I feel like it’s more than last year. We have to improve by far in qualifying. And normally they are strong at Suzuka [where the next race will be held].
"It’s only two weeks away, so we have to be realistic. We can’t improve by that much overnight. We have to take it step by step and avoid making mistakes like we made today."
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