The Portuguese side, who began the game with a 1-0 advantage from last week's first leg, went ahead on the half-hour.
Cheick Diabate levelled the scores on the night with a powerful strike from the edge of the penalty area on 74 minutes.
Parity lasted less than 60 seconds, as Cardozo latched onto Nicolas Gaitan's through ball to restore Benfica's lead.
Jardel then cancelled out his earlier strike with a very unfortunate own goal in stoppage time.
However, Cardozo responded immediately once again to net with a precise finish from 10 yards.