The first start also involved the safety car, with Nico Rosberg's pole position Mercedes following it off the grid with the drivers completing a lap in heavy spray before returning to the pit lane and stopping in a line.
"Lewis is saying the conditions are so poor he cannot see you," Rosberg's race engineer told the German, referring to his team mate and championship leader Lewis Hamilton in second place.
"It was undriveable out there," said Lotus driver Romain Grosjean.
When the rain eased and the race re-started after a delay of some 20 minutes, Ferrari's Fernando Alonso pulled over and stopped with what looked like an electrical failure.
Typhoon Phanfone, lurking off the coast of Japan, had dropped steady rain all morning on the Suzuka Circuit.
Formula One's official forecaster UBIMET had on Saturday predicted a wet race but the brunt of the storm was expected to be felt later on.
That could impact next weekend's Russian Grand Prix if packing up and the transfer of air freight from Japan is affected.
Although support races ahead of the main Formula One event took place on the wet track, the persistent rain made the track treacherous with Force India's Sergio Perez spinning off on his way to the grid.
Rosberg headed into the race trailing Mercedes team-mate and title rival Lewis Hamilton by three points.
(Reporting by Abhishek Takle; Editing by John O'Brien/Alan Baldwin)
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