Nicolas Gaitan fired the hosts in front after nine minutes, levelling the tie on aggregate in the process before a controversial penalty allowed Dirk Kuyt to equalise soon after.
Undeterred, the hosts continued their enterprising efforts up front, with further goals from Oscar Cardozo enabling them to seal their place at the Amsterdam Arena on May 15th.
Benfica coach Jorge Jesus made five changes from the side that lost 1-0 in a frenetic first-leg in Istanbul last week. The likes of Andre Almeida and Enzo Perez returned from suspension, while Salih Ucan replaced the injured Raul Meireles for Fenerbahce.
Given the deficit that the Eagles faced, it was no surprise that the hosts started positively. Oscar Cardozo - ineffectual in last week's clash - brought a good save from Volkan Demirel, before Lima was unable to divert the ball into the net after a brilliant build-up.
Nevertheless, Benfica pulled off their aim of an early breakthrough, amidst a meek opening offered by Aykut Kocaman's men. Lima's mazy run on the right enabled him to pick out the advancing Gaitan, with the Argentine firing the ball superbly in off Volkan's post to level the tie on aggregate inside nine minutes.
Fenerbahce were unusually timid in their approach play, with the Portuguese giants appearing comfortable before a controverisal call from French referee Stephane Lannoy. Kuyt's delivery off Ezequiel Garay was deemed handball by the official, allowing the Netherlands international to slot the ball into the bottom-left corner and silence the stadium.
While that priceless away goal provided an unlikely comfort for the visitors, Benfica continued to press, but were denied two penalty appeals - one similar to Fenerbahce's award - as the game turned sour with three bookings handed out in less than five minutes by the beleaguered referee.
But Benfica's perseverance would indeed pay off by virtue of some quick thinking. From a free-kick, Perez's incisive pass bamboozled the static Fener defence, and allowed Cardozo to fire the ball past Volkan to lead 2-1 on the night, and within one goal of leading on aggregate.
The attacking tempo unrelenting, both sides continued to advance and seek out another goal to aid their final ambitions. Reto Ziegler's cut-back into Kuyt saw the goalscorer hit the side netting, before Nemanja Matic's measured pass into Cardozo whistled narrowly over Volkan's goal in an utterly breathless first half.
The hosts started the second half with the same intensity, and were unlucky not to have scored again. Cardozo picked up the ball on the edge of the area, but this time, the Paraguay international's strike curled inches wide of Volkan's right post.
The night unfortunately took a turn for the worse just before the hour when Gokhan Gonul was stretchered off with what appeared to be a serious injury, after being caught by Gaitan, and that incident appeared to impact on the Turkish side soon after.
From a corner, the undeterred hosts benefitted from a favourable deflection as the ball arrived into the path of Cardozo, who fired easily into the net for his 30th goal of the season, as Jorge Jesus' side finally led 3-2 on aggregate.
Fenerbahce's influence waned, though substitute Miroslav Stoch brought off a decent save from Artur in the Benfica goal, but the Lisbon side held on comfortably to book a place in their first European final since 1990, where they will face Rafa Benitez's Chelsea, who overcame Basel 5-2 on aggregate.
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Benfica 3-1 Fenerbahce: (Agg 3-2) Cardozo double propels Eagles to Europa League final
Nicolas Gaitan fired the hosts in front after nine minutes, levelling the tie on aggregate in the process before a controversial penalty allowed Dirk Kuyt to equalise soon after.