Senna's French teammate Alain Prost was second, with Italy's Ivan Capelli third in a March-Judd after the Benetton-Fords of local driver Thierry Boutsen and Alessandro Nannini were disqualified for fuel irregularities.
Nigel Mansell was forced to miss the race due to chicken pox and was replaced at Williams by Martin Brundle who actually managed to be fastest in the second, wet qualifying session.
The McLaren-Hondas had dominated the first qualifying session and occupied the whole front row for the 7th time in 11 races, though neither Ayrton Senna nor Alain Prost could match Michele Alboreto on the uphill Kemmel Straight as he pushed his Ferrari to 312 km/h (194 mph).
At Spa Prost decided at the last minute to alter the settings on his car by taking off some wing for more straight line speed in a bid to gain an advantage.
Unfortunately for the Frenchman this had a detrimental result and he was unhappy with the balance and handling of his car in the race, compared to Senna with Prost's original settings who reported no such problems.
However, the first time through Eau Rouge, Senna, with better downforce and grip, was clearly quicker and easily retook the lead after he slipstreamed Prost on the Kemmel Straight and out braked him at Les Combes.
Due to Berger's retirement, Boutsen climbed to 4th behind Alboreto and ahead of a thrilling battle between Alessandro Nannini (Benetton), Nakajima, Nelson Piquet (Lotus), and the two Arrows-Megatrons of Derek Warwick and Eddie Cheever.