Tigres UANL became the first team through to the quarter-finals on Tuesday, while Estudiantes drew first blood in their last-16 tie.
A 1-1 draw was suffice for Tigres UANL, who overcame Club Universitario to reach the quarter-finals of the Copa Libertadores.
Tigres held the upper hand heading into Tuesday's return leg after leaving Bolivia with a 2-1 first-leg victory.
And the Mexican outfit sealed their spot in the quarters via a 3-2 aggregate win sealed at Estadio Universitario de Nuevo Leon.
Universitario made the perfect start with barely two minutes played, after Ruben Cuesta's low shot went past Tigres goalkeeper Nahuel Guzman and in off the post.
Tigres restored parity on the night, and put the onus on Universitario to score to force extra time, when Rafael Sobis converted a penalty 15 minutes from time.
The winner of Emelec's clash with Atletico Nacional will face Tigres for a spot in the semi-finals.
Meanwhile, Estudiantes claimed first-leg honours in their round-of-16 match after edging Sante Fe 2-1 in La Plata.
First-half goals from Carlos Auzqui and Guido Carrillo inspired the Argentine hosts at Estadio Ciudad de La Plata.
Auzqui headed Estudiantes into a 21st-minute lead before Carrillo doubled the advantage nine minutes later, side footing past Santa Fe keeper Leandro Castellanos from close range.
Wilson Morelo volleyed Omar Perez's 81st-minute set-piece to give Santa Fe some hope heading into the second leg in Colombia on May 12.