On Honda's home track, the McLarens of Ayrton Senna and Alain Prost filled the front row.
On the third row were the two Lotus-Hondas of outgoing World Champion Nelson Piquet, who was suffering from a virus, and home town favourite Satoru Nakajima, whose mother had died on the Friday morning.
Lotus showed great faith in Nakajima by announcing that they had re-signed him for the 1989 season, despite the fact that they would have to use Judd engines after Honda's decision to supply McLaren exclusively.
French driver Yannick Dalmas was declared medically unfit for the race and was replaced in the Larrousse team by Japan's Aguri Suzuki, who was on his way to winning the 1988 Japanese Formula 3000 Championship.
Dalmas, originally thought to have an ear infection that kept him out of both Japan and the final race in Australia, was diagnosed with Legionnaires' disease later in the year.
On lap 16 Capelli seized his chance to pass Prost for the lead, the first time a non-turbo car had led a Grand Prix since 1983.