The Gabon striker completed his treble with five minutes remaining as he turned in Erik Durm's sublime pass. Dortmund have now lost only one of their last 12 European home matches under coach Thomas Tuchel as they reached the Champions League quarter-finals for the first time since 2014.
Dortmund boss Thomas Tuchel said: "That was the perfect time for 'Auba' to get his hat-trick. "It was a sensational performance. I love goals like his first one because they need such good timing and Auba is always there with his nose for goal. "We had a great start, then we lost our way after 25 minutes, but the second half was a top performance. "We didn't want to let the first-leg defeat annoy us, now we are in the last eight and we want to go further."