The front row was occupied by the McLaren-Honda teammates Ayrton Senna and Alain Prost, marking the team's 11th front-row lockout of the year. Senna took pole position, though his time was 1.8 seconds slower than the 1987 pole time set by Gerhard Berger. Berger qualified third for Ferrari, joined on the second row by Ivan Capelli in the naturally aspirated March-Judd.
The third row featured the Lotus-Hondas of Nelson Piquet and Satoru Nakajima. Piquet participated while suffering from a virus, while Nakajima competed after being informed only 30 minutes before Friday's free practice that his mother had died. During the event, Lotus announced they had re-signed Nakajima for 1989, despite a transition to Judd engines following Honda's decision to supply McLaren exclusively.
Aguri Suzuki made his Formula One debut for the Larrousse team, qualifying 20th. He replaced Yannick Dalmas, who was declared medically unfit and later diagnosed with Legionnaires' disease.
At the start, Alain Prost took the lead while Ayrton Senna stalled his engine. Because Suzuka featured the only sloping grid of the season, Senna was able to bump-start his McLaren and resume the race in 14th place. Senna began an immediate recovery, climbing to eighth by the end of the first lap and reaching fourth by lap 4 after passing Riccardo Patrese, Thierry Boutsen, Alessandro Nannini, and Michele Alboreto.
On lap 5, Ivan Capelli passed Gerhard Berger for second place. As rain began to fall on portions of the track on lap 14, Capelli challenged Prost for the lead. On lap 16, Prost was delayed by the spinning Lola of Aguri Suzuki and subsequently missed a gear due to a malfunctioning gearbox. Capelli passed him to take the lead, marking the first time a naturally aspirated car had led a Grand Prix since 1983. However, Prost used the superior power of his Honda turbo engine to retake the position before the first turn of the following lap. Capelli remained in contention until retiring on lap 19 with an electrical failure.
Senna continued to close the gap to Prost, aided by the wet-and-dry surface conditions and Prost’s gearbox issues. On lap 27, while the leaders were lapping Andrea de Cesaris, Satoru Nakajima, and Maurício Gugelmin, Senna forced his way past Prost as the Frenchman was delayed by de Cesaris's Rial. Once in the lead, Senna broke the lap record and established a three-second advantage.
Despite Senna gesturing for the race to be stopped due to the rain, the event ran its full distance. Senna finished 13 seconds ahead of Prost to take the victory. Thierry Boutsen finished third for Benetton, followed by Gerhard Berger in fourth, Alessandro Nannini in fifth, and Riccardo Patrese in sixth.
Several collisions occurred during the mid-pack exchanges. On lap 5, Derek Warwick and Nigel Mansell collided, necessitating pit stops for a puncture and a new nose cone respectively. On lap 8, Michele Alboreto was forced off the track by Thierry Boutsen while running in sixth place.
Nigel Mansell's race ended on lap 24 following a collision with Nelson Piquet while attempting to lap him. Piquet, who was struggling with double vision and fatigue caused by his virus, retired ten laps later.
Ayrton Senna's victory at Suzuka secured him the 1988 World Championship. Under the scoring system of the time, where only the best 11 results counted, Prost could only reach a maximum of 87 points even with a win in the final round. Although they could have finished equal on points, Senna held the tie-breaker with more wins.
Senna's eighth win of the year surpassed the previous record for most victories in a single season, which had been held jointly by Jim Clark (1963) and Alain Prost (1984) with seven wins. Senna's record stood until 1992, when it was broken by Nigel Mansell.
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