The Gabon international had spectacularly squandered a penalty and half-a-dozen scoring chances in their 1-0 first leg defeat in Portugal last month but he was in stellar form on Wednesday as Dortmund eased into the last eight for the third time in a decade with a 4-1 aggregate victory.
"I had told Auba after the game in Lisbon that he would be the one deciding the return leg. He did just that tonight," Dortmund sports director Michael Zorc said.
The Bundesliga top scorer has now grabbed seven goals in his three matches since the first leg, having scored twice in his previous two Bundesliga games.
He cancelled out Benfica's first leg lead with a fourth minute goal and struck twice more in the second half to take his competition tally to seven goals in seven games.
"Auba had to do the job and he did it," said Dortmund coach Thomas Tuchel. "It was extremely important that he scored twice in the last two league matches.
"You do not need to be scientific about it. You have to score as a forward and then you have a game like in Lisbon where you miss everything there is to miss.
"So it is up to your team mates to help you get out of it and they delivered as well."
Dortmund failed to maintain the intense pressure they had initially piled on after Aubameyang drew them level with a disciplined Benfica, who had won their seven previous matches.
"After our early goal we sort of eased off a bit. Like we lost the plot a bit, too static," said Tuchel, who added he would prefer to avoid German rivals Bayern Munich in the last eight.
Dortmund pulled themselves together and scored twice in three minutes early in the second half to kill off Benfica's hopes of a comeback.
"It was important that we started really well and scored early. We were aggressive but then we seemed to think it would just happen by itself," said Aubameyang.
"At halftime we talked about it and said we need to do more. Three goals and this ball goals to my kids," he said holding the game ball.
(Reporting by Karolos Grohmann, editing by Pritha Sarkar)
