Thomas Tuchel's BVB went into the home leg at the Westfalenstadion a goal down having lost to the Portuguese giants in Lisbon last month but came through with a 4-1 aggregate triumph.
But that was soon pegged back when Pierre-Emerick Aubameyang scored the first of his match-winning hat-trick in just the fourth minute with a simple back-post header which came from a Christian Pulisic flick-on.
Dortmund had to battle away for most of the first half as Benfica sprung into action and the home side's keeper Roman Burki was forced into action to deny a few strong chances, including two from Franco Cervi either side of the break.
But as 59 minutes ticked over, Dortmund scored the goal that saw them go ahead 2-1 in the two-legged tie.
A lovey through ball from Lukasz Piszczek found Pulisic who produced a delightfully deft right-footed chip over an onrushing Ederson Moraes.
This sparked a procession from the Germans as Aubameyang made it 3-0 just a couple of minutes later when he side-footed home a lovely volleyed cross from Marcel Schmelzer.
14 minutes later and the prolific Gabonese striker completed his treble when slotting home with consummate ease from Erik Durm's ball on a platter to wrap it up for Dortmund, sending them through to the final eight of Europe's premier club competition.
2016/17 UEFA Champions League - Round of 16 2nd leg
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