Reigning World Superbike champion Jonathan Rea was in a commanding lead on the #10 Kawasaki having taken the lead from the #33 Red Bull Honda at the start of the final hour of racing.
In the last 20 minutes, the #2 SERT Suzuki expired going into Turn 3, depositing fluid on track, which Rea seemingly hit and crashed with just two minutes left.
The race was red-flagged and Kawasaki initially thought to be the winners, but was thrown out of the result for having failed to make it back to parc ferme within the required five-minute window.
This meant the #21 Yamaha of Alex Lowes, Michael van der Mark and Katsuyuki Nakasuga were declared winners, with #33 Honda and the #1 FCC TSR Honda promoted to third.
Kawasaki subsequently launched an appeal against the result, arguing that the result should be taken from the last completed lap in the instance of a red flag being shown for a clean-up operation.
Initially, race direction declared the result based on those who had made it back to pitlane within the five-minute window.
However, they soon determined that the result should have been declared based on the finishing order from the last completed lap and the five-minute rule disregarded, as the race had not been declared a result at that moment.
This means the #10 team of Rea, Leon Haslam and Toprak Razgatlioglu (who did not complete a stint during the race) were declared winners, and Kawasaki have no achieved its first Suzuka success since 1993.
The #21 Yamaha crew are now officially declared as runner-ups, with the #33 Honda team of Stefan Bradl, Takumi Takahashi and Ryuichi Kiyonari (who was also not run in the race) third.
The only other significant change to the order now is the FCC TSR team losing its rostrum, and is classified fourth again instead.