The second leg was marred by the behaviour of the fans, which caused the referee to abandon the match in the 80th minute with the score 0-0.
Independiente advanced to the Copa Libertadores quarter-finals, where they will face the winner of Racing and River Plate.
After Independiente missed a penalty, local Santos fans began to throw bombs, flares, and other objects onto the field and also attempted to invade the pitch.
The police were able to prevent the pitch invasion, although they used violent force against the enraged supporters.
Carlos Sánchez had been given a red card in his last Copa Libertadores match four years ago with River Plate and never served his suspension, which gave Independiente a 3-0 lead heading into the second leg despite a 0-0 draw on the field.