It was a drama-filled evening after CONMEBOL controversially overturned the result of last week's Copa Libertadores first-leg clash as Independiente advanced to the quarter-finals ahead of Santos.
Santos and Independiente played out a goalless draw on August 21 but the latter were awarded a 3-0 victory just hours before Tuesday's return fixture after the Brazilian side fielded an ineligible player.
Carlos Sanchez was at the centre of the controversy due to a red card he was given during his River Plate stint in 2015, with Independiente arguing the Uruguay international should have been suspended for the opening leg.