Eduardo Salvio ended Newcastle's hopes of continuing their European adventure as Benfica struck deep into injury time, rallying for a 1-1 tie to advance 4-2 on aggregate.
Newcastle was leading 1-0 on the night and pushing for a second goal which would have booked them a semifinal place when Salvio slid home substitute Rodrigo's low cross to secure the tie.
Joining Benfica in the Europa League semifinals is Fenerbache, which held on for a 1-1 tie against Lazio to progress on the basis of a 3-1 win on aggregate in a virtually empty Stadio Olimpico.
Benfica, which started its European campaign in the Champions League, still has not lost in all competitions since October, although they came mightily close to doing so on Tyneside, and they will now head into the last four with ambitions of lifting the trophy.
Newcastle, applauded from the pitch by a crowd of 52,157, will now turn its attention to Sunday's derby clash with Sunderland.
Benfica manager Jorge Jesus appeared so confident of defending a 3-1 first leg lead that he left dangerous frontmen Oscar Cardozo and Rodrigo sitting on the bench. However, it was the visitors who dominated the opening 45 minutes as the anticipated Magpies assault failed to materialize.
Lazio, serving the second of a two-game stadium ban, may not have had its fans to cheer them on but for 70 minutes put up a determined fight to overcome the first-leg deficit, and Senad Lulic's goal just after the hour mark offered hope.
But as Lazio piled forward in search of a second, Caner Erkin's powerful equalizer - their first shot on target - ended Italian hopes and put Fener into the final four of a European competition for the first time.