Robinho, Tiago and Lucas Pratto gave the hosts a 3-0 lead in the first 17 minutes on Thursday before Carlos Carvalho added another goal in the second half at the Mineirao stadium in Belo Horizonte, reports Xinhua.
The result meant Atletico finished the group stage with 13 points, two points ahead of Ecuador's Independiente del Valle, who also qualified for the knockout phase after holding Colo Colo to a 0-0 draw in Santiago.
In other matches on Thursday, Argentina's Rosario Central beat Uruguayan outfit Nacional 2-0 in Montevideo and Palmeiras trounced River Plate of Uruguay 4-0 in Sao Paulo.
Rosario Central and Nacional progressed to the next round while Palmeiras and River Plate of Uruguay were eliminated.
Latin America's top club competition, the Copa Libertadores is contested by teams in South America and Mexico.