Struggling in the Brazil Serie A, Ponte Preta claimed a 2-0 win in Buenos Aires after the first leg of their quarter-final finished 0-0.
Elias and Fernando Bob scored second-half goals for Jorginho's men, who defended resolutely after half-time at the Estadio Jose Amalfitani.
Ponte Preta will face Sao Paulo in their semi-final, while Libertad meet Lanus for a place in the decider.
Involved in a relegation battle domestically, Ponte Preta secured a surprise win at Velez Sarsfield.
The hosts had looked the more likely to score before Elias struck on 49 minutes after a fast counter-attack.
Elias exchanged passes with Rildo on the break before placing a smart finish past Sebastian Sosa in a one-on-one.
Velez Sarsfield put the pressure on and had several opportunities from corners, only for the visitors to seal victory in the second minute of additional time.
Fernando Bob was released on the break and had his initial shot saved by Sosa but was on hand to nod into an open net.
Adrianinho, an unused substituted, was red-carded for Ponte Preta after the sealer.
Libertad completed a 2-1 aggregate win over Itagui despite suffering a 1-0 loss in Colombia on Thursday.
Gustavo Bolivar scored the only goal of the game on 19 minutes but the hosts were unable to find a second on a wet Estadio Polideportivo Sur pitch.
