Universidad de Chile, Libertad and Internacional secured the remaining spots in the Copa Libertadores quarter-finals.
Universidad, who had won the first leg against Alianza Lima 1-0 had to suffer more than expected at home, and only a controversial goal in stoppage time saw them progress.
The Peruvians took the lead in the 24th minute through Jose Fernandez before Eduardo Vargas' second-half equaliser.
Alianza looked to have won the tie when Fernandez grabbed his second of the night four minutes from time but, a minute into stoppage time, Felipe Seymour levelled with two of his team-mates seemingly off-side.
Alianza players and staff protested fiercely but to little avail and, to add insult to injury, referee Carlos Vera then dismissed two of the visiting players.
In Paraguay, Libertad also needed a last-gasp winner to eliminate Colombia's Once Caldas.
After a goalless draw in the first leg, the Colombians went ahead with a 54th-minute goal by Dayro Moreno before Roberto Gamarra levelled from the spot in the 72nd minute. And Gamarra pounced again in the final minute to send Libertad through.
Internacional join them in the final eight on the away goals rule following a 2-0 victory over Banfield.
The Brazilian outfit had lost 3-1 in Argentina but Alecsandro and Walter Henrique scored tonight to book them a tie against defending champions Estudiantes.