Gaston Fernandez gave the Argentines the lead in the first minute but Libertad took control and were threatening an equaliser when Brazilian referee Carlos Simon awarded the hosts a penalty in the 62nd minute.
Miguel Samudio was judged to have fouled Marcos Angeleri as he cleared the ball. Samudio, who protested vehemently, was sent off and Mauro Boselli converted.
Boselli added a third for the three-times champions when he headed in Juan Sebastian Veron's cross in the 70th minute of Thursday night's game in La Plata.
Cruzeiro continued the impressive form of Brazilian clubs by winning 2-1 away to Universidad de Chile in Santiago.
Soares and Marquinhos Parana scored early in each half for Cruzeiro and Manuel Villalobos pulled one back with five minutes left.
Universidad had Rafael Olarra sent off in the 87th minute for a second yellow card.
Deportivo Cuenca striker Rodrigo Teixeira scored his seventh goal of the competition as the Ecuadoreans beat Venezuelan champions Caracas FC 2-1 at home.
Teixeira converted a penalty in the 57th minute to wipe out Gabriel Cichero's third-minute strike for the visitors, who had Rafael Castellin sent off after only 20 minutes for elbowing.
Ismael Villalba scored Cuenca's winner on a rain-soaked pitch in the 69th minute.
