Oscar Piastri topped the timing sheets of free practice two that had four red flags in what was a manic session.
Teams and drivers had their planned runs scuppered due to three red flags that wiped out the majority of the session time.
Jack Doohan was the first to bring out the red flag after just ten minutes, flying off at turn 1 to crash into the wall side-on and severely damage his Alpine, completing four laps on Friday after Ryo Hirakawa took the Australain's seat in FP1.
Fernando Alonso was the next to bring out the red flag to bring a stop to the session, putting a wheel of his Aston Martin onto the grass going into turn 8, meaning he lost control and spun out into the gravel, keeping himself out of the barriers to reduce the amount of damage done.
The final two red flags that occurred came from two fires caused by sparks that lit up the grass, setting the outside of the track alight to give a real worry to the organisers at Suzuka.
As a result of all those stoppages, some drivers were not even able to get their soft tyre running in, but Piastri was able to do so, going +0.049 quicker than his teammate Lando Norris.
Racing Bulls driver Isack Hadjar rounded out the top three with a fine lap, coming ahead of Lewis Hamilton in P4, while Liam Lawson in the other Racing Bull finished in fifth.
George Russell and Charles Leclerc were in P6 and P7, respectively, while Max Verstappen could only manage P8 with his soft tyre lap, with both Racing Bulls ahead of him.
Pierre Gasly and Carlos Sainz rounded out the top then, while Yuki Tsunoda came down in P18, not able to get a soft tyre lap in, like Kimi Antonelli down in P16.