As Boca Juniors and River Plate had already qualified, Rosario Central and San Lorenzo (2nd and 4th respectively) earned their right to play the Copa Libertadores.

On the other hand, Talleres de Córdoba replaced Gimnasia y Esgrima to play the 1999 Copa Conmebol after the club from La Plata declined to participate.

As a result, three teams were relegated, Ferro Carril Oeste, Gimnasia y Esgrima (J) (worst averages) and Instituto (C) (lost promotion to Almagro).

The system ruled that clubs with the third and four worst averages played a two-legged series versus two teams qualified from Primera B Nacional.

Instituto and Belgrano (both from Córdoba) played the promotion playoff v Almagro and Quilmes (qualified from 1999–2000 Primera B Nacional) respectively.