The Portuguese club were beaten 1-0 in Istanbul last week but fought back to book their spot in the May 15 decider in Amsterdam against the current Champions League holders.
With the tie in the balance, Oscar Cardozo took things into his own hands by edging Benfica ahead 2-1 on the night and levelling the tie at 2-2 in the 35th minute with a low left-footed finish after a free-kick found him on the edge of the area.
The Paraguayan then gave Benfica an overall lead just after the hour-mark when he was on hand to control beautifully and then rifle home much to the delight of the Estadio da Luz faithful.
It was a tense finish for Benfica as Fener required a second goal on the night to progress on away goals but they were unable to do so with Jorge Jesus' Eagles doing enough to book a date with Chelsea in a few weeks' time.
2012/13 UEFA Europa League semi-final - second leg
Estadio da Luz, Lisbon - 55,402