Gustavo Lorenzetti's 82nd-minute winner was enough for 2011 Copa Sudamericana champions Universidad Chile to edge Defensor Sporting 1-0 at the Estadio Nacional Julio Martinez Pradanos.
The 28-year-old Argentine sent the home fans wild when he drilled in from the edge of the area after a corner had been cleared.
Universidad Chile are second in Group 5, which is topped by Real Garcilaso after their win on Wednesday.
High-flying Colombia Primera A outfit Atletico Nacional left it late to overcome Newell's Old Boys 1-0 in Medellin.
The Argentines look set to take a point from the Group 6 clash before Edwin Cardona's 30-yard effort snuck into the bottom corner.
In the other Group 6 match, Cristian Riveros struck on 69 minutes to lead Gremio to a 1-0 win over Nacional at the Estadio Gran Parque Central in Montevideo.
On a day of few goals, Atletico Paranaense were 1-0 winners at home to The Strongest thanks to a 24th-minute goal from Paulinho Dias in Group 1.
In Group 3, Lanus and O'Higgins played out a 0-0 draw.
The only game to feature more than one goal on Thursday was Emelec's come-from-behind 2-1 win at home to Bolivar.
Juanmi Callejon opened the scoring on 11 minutes, cutting inside from the left and past two defenders before firing home.
Angel Mena levelled a minute later as he tucked away Marcos Caicedo's cutback and there were no other goals in Guayaquil until late on.
Fernando Gimenez powered in a header from Fernando Gaibor's corner to score the winner on 74 minutes, putting Emelec top of Group 7.
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