There were three weeks between the Spanish and Japanese GPs and there were several changes in the entry. Sandro Nannini had been seriously injured in a helicopter accident, his right arm being severed just below the elbow by the disintegrating rotor blade. This was reattached in an 11-hour operation that evening in Rome and, although it was "a technical success", Nannini would never race in F1 again, although he did recover enough to race touring cars successfully. He was replaced by Roberto Moreno, EuroBrun having withdrawn from F1 (along with the Life team). Martin Donnelly was still in intensive care after his accident in Spain and so Johnny Herbert had been signed up by Team Lotus. Paolo Barilla had left Minardi as well, opening the way for Gianni Morbidelli. With only 30 cars there was no need for pre-qualifying.

The system of pre-qualifying was developed in response to the increasing number of teams competing in Formula 1. It was decided that 30 cars were the maximum safe limit to compete for 26 grid places. The cars which had to pre-qualify were decided at the beginning and the midpoint of each season. The 26 cars which had achieved the best results in the previous two-half seasons automatically entered official qualifying for the race. All the other cars had to pre-qualify for the four other slots available for official qualifying. Those that failed to pre-qualify just went home.

There were a number of big crashes in qualifying with Emanuele Pirro dislocating a finger when he crashed his Dallara and Jean Alési hurting a neck muscle when the Tyrrell went off at the first corner, skipped the sandtrap and hit the wall head-on. He took no further part in the weekend.

In a splendid qualifying showdown, McLaren's Ayrton Senna just beat his World Championship rival Alain Prost (Ferrari) to pole position. Nigel Mansell (Ferrari) and Gerhard Berger (McLaren) were on the second row ahead of Thierry Boutsen (Williams) and Nelson Piquet's Benetton. Then came Alési (who would not race), Riccardo Patrese (Williams) and Moreno. The top 10 was completed by Aguri Suzuki (Lola Larrousse Lamborghini) and Pierluigi Martini's Minardi.

Overnight there had been a political battle going on over pole position. McLaren wanted it to be changed so that Senna would be on a clean piece of track but the request was blocked. Senna saw it as collusion between Prost and the officials and it helped to decide him on a frightening course of action at the start. If his position proved to be a disadvantage Senna was not going to back off in the first corner. Prost made the better start (as expected) and as they went into the first corner he was half a car length ahead. Senna went for the gap and did not lift off. The two cars collided and spun into the sand trap. Senna was the World Champion. With once race left, Prost would not be able to get the points necessary to beat him. The incident put paid to Stefano Modena's Brabham which ran into Philippe Alliot's Ligier in the sand cloud and the two Arrows contrived to run into each other, which dropped Michele Alboreto to the back of the field.

Out in front Berger led but at the start of the second lap Gerhard spun off on sand from the incident. This left Mansell being chased by the two Benettons, with Piquet and Moreno more or less holding station and keeping the Williams-Renaults at bay. On lap 26 Mansell pitted. He had a healthy lead but was in a hurry to get out of the pits as both the Benettons and Patrese's Williams were running on the harder B compound tyres, trying to go through without a stop. It was a quick stop and Mansell set off with a huge burst of horsepower which snapped the Ferrari driveshafts. This left Piquet and Moreno first and second with Patrese in third. Riccardo soon realized that the tyres were not going to go the distance and so pitted and Suzuki moved to third place. Patrese, Boutsen and Satoru Nakajima (Tyrrell) completed the top six.