The defender popped up with 18 minutes to go to prod home the winner after a controversial decision from the fifth official decided a narrow semi-final against the Portuguese
In a match which saw attacking action primarily against the woodwork, which was to be hit a surprising five times, Egemen Korkmaz's controversial late winner pushed the Turkish hosts that little bit closer to Amsterdam and a first-ever European final.
On a night of frustration for Benfica, substitute Nicolas Gaitan got closest with a shot against the post, with the visitors having it all to do at Estadio da Luz next week.
Aykut Kocaman made two changes from the side that dismantled Lazio in the quarter-final, with Moussa Sow returning to start alongside Pierre Webo and Dirk Kuyt. On the opposite side, Jorge Jesus deployed five changes to the starting eleven that beat Newcastle as captain Luisao missed out through a thigh injury.
Despite the typically raucous atmosphere inside the Istanbul venue, it proved to be a cautious opening to the semi-final, with both sides happy to bide their time as Eduardo Salvio and Maxi Pereira ensured Benfica enjoyed the better start.
But given Fenerbahce's tidal wave of support, it was not long before they rallied at the other end with chances coming in quick succession.
Firstly, Webo's neat pass into Sow flashed narrowly wide, before Kuyt's superb cross was met wonderfully by the Ivorian striker who easily beat Jardel in the aerial challenge, though was unlucky to see his bullet header cannon back off the crossbar.
Still, Kocaman's side threatened continously as the Eagles appeared in danger of falling behind. Egemen Korkmaz did well to find space and grind out a free header which was headed tamely at Artur, despite a good set-piece delivery from the hosts, who by now were in the ascendancy.
Nevertheless, the Portuguese visitors hit back at the other end, with surprise starter Pablo Aimar pulling the strings as Ezequiel Garay saw a decent chance wasted with Oscar Cardozo surprisingly quiet up front before the first-half drama began to ensue in additional time.
Ola John was adjudged to have fouled Gokhan Gonul approaching the penalty box, with Serbian referee Milorad Mazic immediately pointing to the spot. Up stepped Cristian Baroni, whose low penalty slammed against the post and away on the stroke of half-time, with the midfielder being dragged away in tears by team-mates to complete a high-tempo first half.
The second, however, started in the same way for the Turkish outfit who were once more unable to penetrate the defence. With Cristian once more bringing a fine save out of the goalkeeper, followed by Raul Meireles' stinging effort, Kuyt fired a third effort against the woodwork with a fine swivel and shot which Artur eventually got to.
The attacking intensity unrelenting, it was time for Benfica to test the vulnerable Volkan in the opposite goal, with Cardozo smashing a low effort towards the goalkeeper, before subsitute Nicolas Gaitan ensured the post was hit for the fourth time with a great effort from outside the box which left the keeper stranded.
The deadlock was finally broken in controversial circumstances as the game hurtled towards the final quarter of an hour. From a corner, Korkmaz rose highest to head the ball yet again off the post with Melgajero at fault as the ball crossed the line before celebrations got going after the fifth official awarded the goal.
Fenerbahce held on to take command of the semi-final tie, as they look to confirm their place in the Europa League final next week in the semi-final second leg at Estadio da Luz.