The first phase was disputed by all the teams of the championship, save for Corinthians, Palmeiras, Santos and São Paulo, which would dispute the Rio-São Paulo tournament at the time and would only enter in the second phase. The teams would be divided in two groups of six teams, and the four best teams in each group would qualify for the second phase, with the others going to the relegation group.
Updated to match(es) played on 20 June 1999. Source: RSSSF.com Rules for classification: 1) points; 2) goal difference; 3) number of goals scored. (A) Advance to a further round; (E) Eliminated
Updated to match(es) played on 20 June 1999. Source: RSSSF.com Rules for classification: 1) points; 2) goal difference; 3) number of goals scored. (A) Advance to a further round; (E) Eliminated
Updated to match(es) played on 20 June 1999. Source: RSSSF.com Rules for classification: 1) points; 2) goal difference; 3) number of goals scored. (R) Relegated
Second phase
In the second phase, the 8 qualified teams were joined by the four participants of the Rio-São Paulo tournament. The 12 teams were divided in two groups of six teams, with each team playing twice against the teams of its own group, and once against the teams of the other group, with the two best teams in each group qualifying to the Semifinals.