But the rain, which had been spitting very lightly from the start, began to get heavier on lap 29, lap times dropped by around two seconds, and by lap 31 Schumacher had the lead back down to 1.1sec, and down to 0.9sec on lap 32.
The German won his eighth victory of the 16 races so far this season to put his championship lead beyond the reach of his title rival Mika Hakkinen with one race still to go.
The victory puts Schumacher into the exclusive ranks of triple world champions and ends a drought that has at times made the well-funded Italian team the laughing stock of F1.
Schumacher, who has been trying to win the title with Ferrari since 1996, said: "It is difficult to put the feeling into words. I had a lot of emotions as I crossed the line.
His win came as a result of light rain falling in the crucial middle section of the race, between the first and second pit stops.
The rain master
In conditions in which Schumacher has made his reputation as the best driver in the world, he made up crucial extra time on Hakkinen just before his second and final pit stop, which came three laps after the Finn's.
That enabled the German to rejoin the track with a comfortable four-second lead over Hakkinen's McLaren.
Hakkinen had appeared to have a slight but potentially decisive advantage when the track was bone dry, and he was holding a lead of a little over two seconds by lap 28.
But the rain, which had been spitting very lightly from the start, began to get heavier on lap 29, lap times dropped by around two seconds, and by lap 31 Schumacher had the lead back down to 1.1sec, and down to 0.9sec on lap 32.
By lap 34 the rain had eased off again and Hakkinen began to re-extend his lead slowly, but he was committed to a second stop on lap 37, while Schumacher had been given enough fuel for another three laps.
At the same time, rain started to increase slightly in intensity around the demanding Suzuka track, and the German, who has an incredibly sure touch on a damp track, was able to capitalise on his genius in the conditions.
Heavier fuel load
He put in three storming laps, while Hakkinen, with a heavier fuel load, was more tentative, and Schumacher rejoined with a lead of 4.1sec.
Heavier rain in the last six laps merely served to strengthen Schumacher's grip on the race.
Before the rain, it had appeared to be Hakkinen's race. The 31-year-old took the lead at the start despite a desperate attempt by Schumacher to keep him behind.
The German made a bad start and lunged across the track at Hakkinen. But the McLaren was already alongside and Schumacher could not hold him back.
Just as in qualifying on Saturday, Hakkinen and Schumacher were in a league of their own, lapping within tiny fractions of a second of each other, well out of reach of the rest of the field.
But by lap nine there were the first signs that Hakkinen had the edge on Schumacher. His lead was out to over 1.5secs and he was pulling out about 0.1sec a lap.
On lap 11, one-fifth of the distance, Hakkinen got the lead out to over two seconds for the first time, and he continued to creep away until he was about 2.5secs ahead at the first pit stops.
Stunning
Hakkinen stopped on lap 22 with Schumacher coming in a lap later, and the Finn was comfortably able to re-take the lead before the Ferrari regained the track, after doing a stunning time on his first lap out of the pits. But Ferrari had put more fuel in Schumacher's car and that was to prove crucial.
The rest of the field were nowhere.
McLaren's second driver, David Coulthard, finished third, with Ferrari number two Rubens Barrichello fourth.
That gives Ferrari a 13-point lead in the constructors' championship, all-but giving it victory in that as well, with a maximum of 16 points available at the final race in Malaysia on 22 October.
Williams-BMW is in an even stronger position in third. It is now 16 points ahead of Benetton, which can only take the place if it finishes first and second at Sepang, an extremely unlikely eventuality.
Jacques Villeneuve finished sixth for British American Racing, to give it a slender one-point lead over rivals Jordan in the battle for fifth place.
Leading results Japanese Grand Prix:
1 Michael Schumacher (Ger) Ferrari
2 Mika Hakkinen (Fin) McLaren
3 David Coulthard (GB) McLaren
4 Rubens Barrichello (Bra) Ferrari
5 Jenson Button (GB) Williams
6 Jacques Villeneuve (Can) BAR
Drivers' world championship:
1 Schumacher 98 points
2 Hakkinen 86
3 Coulthard 67
4 Barrichello 58
5 Ralf Schumacher (Ger) Williams 24
6 Giancarlo Fisichella (Ita) Benetton 18
7 Villeneuve 15
8 Button 12
9 Heinz-Harald Frentzen (Ger) Jordan 11
10 Jarno Trulli (Ita) Jordan 6
Constructors' championship:
1 Ferrari 156
2 McLaren 143
3 Williams 36
4 Benetton 20
5 BAR 18
6 Jordan 17
* McLaren were docked 10 constructors points after the French Grand Prix, but Hakkinen was allowed to keep drivers' points.