Rain had been forecast for Sunday throughout the weekend, and started falling around an hour before the start of the race at 2pm local time in Japan.
Conditions stabilised so that drivers were able to take a regular standing start, all starting on the intermediate tyres, but the high amount of spray meant that visibility was limited.
The opening lap saw Carlos Sainz crashed out of the race, aquaplaning at the exit of the hairpin, while Sebastian Vettel and Zhou Guanyu also spun in the damp conditions.
The safety car was deployed before the drivers came around to start the second lap, before this was eventually upgraded to a red flag one lap later.
All cars have returned to the pit lane, where teams have been permitted to erect gazebos to keep them dry during the rain delay.
Should conditions remain wet, it is likely the eventual resumption will be a rolling start after laps behind the safety car.
Prior to the red flag, Pierre Gasly was the only driver to have pitted for full wet tyres after requiring a nose change when an advertising hoarding got stuck on the front of his car during the opening lap.
Pole-sitter Max Verstappen will lead the field away whenever the race does restart. Despite momentarily losing the lead of the race to Charles Leclerc off the line, Verstappen managed to hang his car around the outside at Turn 1 and regain P1.
Should Verstappen outscore Leclerc by eight points and Red Bull teammate Sergio Perez by six points, he will clinch his second F1 world title on Sunday at Suzuka.
Sainz's crash allowed Perez to move into the top three for Red Bull ahead of the red flag. He will restart the race ahead of Esteban Ocon in fourth place, while Lewis Hamilton and Fernando Alonso sit fifth and sixth as things stand.
Lance Stroll was one of the biggest gainers on the opening lap, charging from 18th on the grid all the way up to 11th after shooting up the inside of a number of cars into Turn 1.
Carlos Sainz said he "still doesn't know" why we "keep risking" having a tractor out on track, especially considering the race was red-flagged shortly after.
The Ferrari driver said: "I don't know if people understand, but even behind the safety car, we are going at 100-150 kph, and still at those speeds, we don't see nothing, even behind the safety car.
"If one driver decides to get a bit out of the racing line or has a small aquaplaning or has to change a switch on the steering wheel and gets a bit out of line, and hits a tractor, then it's over, no?
"I still don't know why in these conditions we keep risking having a tractor on-track, because it's just worthless. If you're going to red flag it anyway, why risk it?"
