Max Verstappen took victory at Suzuka in difficult conditions ahead of Charles Leclerc and Sergio Perez.
The victory secures Verstappen his second world title after full points were awarded following the restart.
The red flag was brought out after Carlos Sainz crashed on the exit of Spoon Corner, after the F1-75 aquaplaned off fighting with Sergio Perez for third.
After nearly two hours sat in the pit lane waiting for conditions to improve, the race was restarted when the rain eased up.
With 40 minutes left on the clock the drivers were led around briefly by the Safety Car, before going back to green flag conditions.
Drivers take early advantage of Intermediate crossover
As the conditions eased the drivers started think about Intermediate tyres, with Nicholas Latifi and Sebastian Vettel making quick use of a pit stop early on.
As they started to set purple sectors the leaders followed suit, with only Fernando Alonso and Mick Schumacher staying out for an extra couple of laps.
Meanwhile the early stops put Latifi and Vettel in contention for a top 10, as the midfield runners lost time with teams double-stacking their cars.
Verstappen assumed the lead of the race again and started to stretch the gap to Leclerc by nearly two seconds per-lap.
The Ferrari driver fell into the clutches of Perez towards the end, while Lewis Hamilton also battled Esteban Ocon for fourth.
The Mercedes struggled on straight line pace to get alongside the Alpine for a move, eventually settling for fifth on the road.
George Russell meanwhile made progress after losing out in the first round of stops, overtaking both Latifi and Lando Norris for eighth place.
Leclerc penalty hands Verstappen title
Alonso made a late stop for a new set of Intermediates to try and improve his position, however he was only able to improve to seventh despite the late comeback passing Norris, Latifi and Russell.
Leclerc meanwhile was battling with Perez towards the end for second. The pair took it to the last lap, with the Ferrari driver cutting the final chicane which earned him a five-second post-race penalty, promoting Perez to second.
That penalty coupled with the full points being awarded enabled Verstappen to take his second world championship.
Result Race - Japanese
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