Colombia Wrap: Atletico Nacional stay unbeaten
Sherman Cardenas scored the only goal of the game on 65 minutes for Juan Carlos Osorio's men.
The reigning Apertura champions have started the season in stunning style, streaking to the top of the standings with five wins and a draw.
Three teams are in second place on 14 points including Millonarios, who needed a stoppage-time winner to fend off Atletico Huila 3-2.
Huila have struggled so far with only one win in their first eight games but were buoyed by Luis Paez's 12th-minute opener.
The lead only lasted 14 minutes when Dayro Moreno equalised before Dawlin Leudo handed Millonarios the advantage a minute later.
It seemed as if Millonarios would hold on for victory but Mario Leguizamon's 81st-minute strike levelled the contest for Huila.
There was yet another twist on 92 minutes as Moreno completed his brace, handing Millonarios their fifth consecutive win.
Deportivo Cali joined Millonarios on 14 points after a narrow 1-0 victory over Itagui.
An 82nd-minute goal to Carlos Lizarazo was enough to secure the points for Cali.
In other matches, Envigado drew 2-2 with Boyaca Chico, Patriotas Boyaca won 3-0 against Deportes Quindio and Medellin fought out a goalless draw with Deportivo Pasto.
Once Caldas and Alianza Petrolera finished 1-1, while La Equidad drew 0-0 against Cucuta Deportivo.