The World Championship had been settled in Portugal and winner Alain Prost had announced his retirement from F1 at the end of the season. In the month between the Portuguese and Japanese races much was happening. McLaren signed a deal to use Peugeot engines in 1994, while it was announced that Ayrton Senna would finally leave the team to join Damon Hill at Williams. Pedro Lamy would stay on with Lotus as Alex Zanardi was still not ready to return as a result of his crash in Belgium. Eddie Irvine came in to partner Rubens Barrichello at Jordan while Minardi replaced Christian Fittipaldi with Frenchman Jean-Marc Gounon, while Philippe Alliot was dropped by Larrousse to make way for Japanese veteran Toshio Suzuki.

Ligier turned up with an unusual Gitanes color scheme for Martin Brundle's car but there were signs of trouble ahead as team boss Cyril de Rouvre attacked a journalist who had written that he was in legal trouble in France.

Alain Prost was fastest as was normal but Damon Hill spun in qualifying and so had to be satisfied with a lowly sixth on the grid. This allowed Ayrton Senna to take second on the grid in his McLaren-Ford with his new team mate Mika Häkkinen third ahead of Michael Schumacher's Benetton, Gerhard Berger's Ferrari, Hill, Derek Warwick (Footwork) and Irvine, a Suzuka expert. Jean Alési had a heavy accident in his Ferrari and was 14th on the grid.

In the race Senna made the best start and led Prost and Häkkinen with Berger fourth and a fast-starting Irvine fifth, although he was soon pushed back to seventh by a slow-starting Schumacher and by Hill. Alési blew an engine early on and Schumacher followed him into retirement after making contact with Hill when both men tried to challenge Berger. The first pit stops had already begun when it started to rain but it was not wet enough for a tyre change and in the conditions Senna was quickly able to close up on Prost. Hill's hopes of a good result were ruined with a puncture which meant he had to stop for slicks but then two laps later the rain had increased and he was back for wets. When Prost, Senna and Häkkinen pitted for wets, Prost's stop was slow and so Senna went ahead. The rain then eased and the track began to dry and in the difficult conditions both Prost and Hill went off but were able to rejoin. Patrese (Benetton) also had a brush with another car and damaged an oil cooler. Later in the race this broke and Patrese spun at high speed and was fortunate to escape without injury from a huge accident.

Senna and Prost battled for the lead and the gap closed dramatically when they came up to pass the battle for fifth place between Hill and Irvine. Irvine greatly annoyed Senna with his behavior and after the race the two came to blows. The leaders eventually got clear of the Ulsterman and soon afterwards pitted for slicks. The order at the front was set with Senna leading home Prost and Häkkinen to score his 40th and McLaren's 103rd victory, equalling Ferrari's record of Grand Prix wins. Hill managed to extricate himself from the clutches of the cocky Irvine who also annoyed Warwick by punting him off at the chicane with three laps to go. In the end fifth place went to Barrichello with Irvine sixth.