After a goalless draw in the first leg last week, Hernan Torres' Tolima claimed a crucial triumph in Colombia with second half goals to move into the all-important group phase.
Danny Santoya opened the scoring 20 minutes after the interval after he was assisted by Elkin Murillo, then Corinthians midfielder Luis Ramirez was sent off in the 70th for using his elbow.
Finally in the 77th minute, Murillo crossed the ball and Wilder Medina headed the ball into the back of the net.
The 2009 Copa Libertadores and reigning Argentinian champion Estudiantes, Brazilian giant Cruzeiro and Guarani of Paraguay will be Tolima's rivals in Group 7.
In Porto Alegre, Gremio came back from a goal down to celebrate a 3-1 home win over Uruguay's Liverpool. It was a 5-3 aggregate win.
Emiliano Alfaro put Liverpool ahead in the 35th minute, but Andre Lima equalised three minutes later by heading a Fabio Rochemback free-kick in.
Nine minutes into the second half, Liverpool midfielder Michel Acosta was sent-off as he tackled Andre Lima while two goals from Vinicius Pacheco, in the 58th and 74th minutes, gave Gremio the victory.
Gremio will play in Group 2 alongside Bolivian club Oriente Petrolero, Colombia's Junior and Leon de Huanuco of Peru.