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Teams were divided into 3 groups of 3 teams each. The teams would play against each other on a home-and-away basis. The 2 group winners with the best record would qualify. The group winner with the worst record would advance to the CONMEBOL / OFC Intercontinental Play-off.
Draw
The draw for the qualifying groups took place in Zürich, Switzerland on 12 December 1987. During the draw teams were drawn from 3 seeded pots into the 3 qualifying groups.
The match was abandoned in the 67th minute with Brazil leading 1–0 after Chile walked off the field when a firecracker thrown from the crowd supposedly hit goalkeeper Roberto Rojas in the head, leaving him bloodied and having to be carried from the pitch on a stretcher; a subsequent FIFA investigation found that Rojas's injury was self-inflicted, using a razor blade concealed in his glove. On 13 September, the match was awarded 2–0 to Brazil, and Chile were banned from qualifying for the next World Cup. Rojas was given a lifetime ban from competitive football (lifted in 2001), as was Chile manager Orlando Aravena, vice-captain Fernando Astengo and team doctor Daniel Rodriguez.
The Chile–Venezuela match was played on neutral ground in Argentina instead of in Chile because Chile was penalised for rioting during the Chile vs Brazil match.