Alianza were minutes away from qualification on the away goals rule, leading 2-1 at the Monumental in Santiago having lost the first leg at home in Lima 1-0 last week.
But a shot by Felipe Seymour two minutes into stoppage time was deflected off a defender past Alianza goalkeeper George Forsyth into the net to give The U a 2-2 draw and send them through instead 3-2 on aggregate.
Alianza were incensed because the linesman signalled for offside at first but after consultation with the referee Carlos Verase the goal was allowed to stand. The Peruvians argued that Chilean players in offside positions blocked Forsyth's vision, a view backed up by video replays.
The visiting team's Argentine coach Gustavo Costas was incensed while riot police formed a protective wall around the match officials in the middle of the pitch as Alianza players tried to argue with them.
Play was held up for more than a quarter of an hour before the referee resumed the match, playing out the remaining two minutes of stoppage time in a climate of hostility from the Monumental crowd towards the visitors.
FIRST CONTROVERSY
The only man sent off before play resumed was Costas when the referee might have had grounds for more dismissals even if the anger, pushing and shoving never boiled over into a free-for-all. The home players keep out of the argument.
Alianza, the better team on the night, were unlucky not to go through having scored twice through striker Jose Fernandez, his second goal coming in the 86th minute.
The Peruvians were fortunate, though, with Fernandez's first goal in the 25th minute, a header at the far post that Universidad de Chile's keeper Miguel Pinto palmed away without the ball appearing to have crossed the line but which the linesman ruled had gone in.
Eduardo Vargas scored the first equaliser just past the hour for the home side, who go on to meet Brazilian champions Flamengo in the quarter-finals next week. The two sides met in the group phase with the Chileans winning at home and drawing away.
Brazil's Internacional, South American champions in 2006, beat Argentina's Banfield 2-0 to go through on the away goals rule having lost the first leg 3-1 in Buenos Aires last week.
Inter now meet title holders Estudiantes, the only remaining Argentine side in the competition.
Libertad of Paraguay came from a goal down to beat Colombia's Once Caldas 2-1 in Asuncion with two goals from substitute striker Roberto Gamarra to go through by the same score on aggregate to meet Guadalajara of Mexico.
The other quarter-final is between Brazilian sides Cruzeiro, and Sao Paulo, who both qualified on Wednesday.
