A late Michael Rangel brace helped Envigado to a 2-0 win at Alianza Petrolera and into sixth in the table, with the top eight going into the quarter-finals.
Rangel opened the scoring on 82 minutes and added another soon after to seal the result for Juan Sanchez's men.
Finishing behind Envigado were Itagui and La Equidad despite the duo failing to win on matchday 18.
Itagui came from behind twice to draw 2-2 at home to Once Caldas, with the sides finishing seventh and fifth respectively.
La Equidad suffered a shock 1-0 loss at Deportivo Cali, but their nearest rivals failed to take advantage.
Alianza Petrolera were one of those teams, while Boyaca Chico ended up 10th after their 2-1 loss at Medellin.
Atletico Nacional finished top of the table despite suffering a 2-1 loss at Patriotas Boyaca, who climbed off the bottom.
The league leaders had looked the more likely to open the scoring away from home.
But after missing several chances, they were made to pay as Carlos Renteria tucked away a neat finish from a corner.
Renteria doubled the lead on 72 minutes when he got on the end of an Antonio Otero goal-kick and delightfully chipped goalkeeper Christian Vargas from 25 yards.
Jairo Palomino headed in a set-piece for Atletico Nacional three minutes later, but they were unable to find an equaliser.
Millonarios and Junior finished second and third respectively – a point behind – after claiming wins.
Junior edged fourth-placed Santa Fe 2-1 and Millonarios clinched a come-from-behind 3-1 win over bottom club Deportes Tolima.
Atletico Huila and Uniautonoma drew 1-1 and Fortaleza cruised to a 4-1 victory over Deportivo Pasto.
