 The Group Stage saw Deportes Tolima getting a dramatic 2-1 win over Atlético Nacional thus becoming leaders of Group A while in Group B, Independiente Medellín thrashed Millonarios 4-0 in the Estadio Atanasio Girardot only to learn that Cúcuta Deportivo and Atlético Huila tied 0-0.The champions were Cúcuta Deportivo defeating Deportes Tolima in the finals with the total aggregate score of 2-1 from two matches.Standings until November 16, 2006

 Pts=Points; GP=Games played; W=Wins; D=Ties; L=Losses; GS=Goals scored; GA=Goals allowed; DIF=Goal difference

The second phase of the 2006-II Copa Mustang consisted of the quadrangular phase or semifinals.