The home side continued to press in the second period and they had their third after 66 minutes when Cardozo added his second of the night from close range.
Both sides had half-chances in the latter stages, but Fenerbahce could not add to their tally as the Portuguese outfit booked their spot in the final, where they will face Chelsea.
Read how it all unfolded in Sports Mole's minute-by-minute live commentary of the action below.
BENFICA: Artur; Pereira, Luisao, Garay, Almeida; Perez, Matic, Gaitan, Salvio; Lima, Cardozo
FENERBAHCE: Volkan; Gonul, Yobo, Korkmaz, Ziegler; Cristian, Sahin, Ucan, Erkin; Kuyt, Sow