Few would have backed Tottenham to turn around this last-16 tie at White Hart Lane against the in-form Bundesliga giants.
The damage was done seven days earlier in Germany when Spurs manager Mauricio Pochettino decided to play a weakened and inexperienced team against one of the favourites to win the Europa League.
But the reasoning behind the Argentine’s decision was clear – his main priority this season is leading the north London club to the English league title for the first time since 1961.
Second-placed Tottenham are five points behind Premier League leaders Leicester and, with another important top-flight game looming against Bournemouth on Sunday, Pochettino again decided to leave top scorer Harry Kane on the bench.
Without their talisman, the home side never looked like troubling a Dortmund team which had not been beaten in their 13 previous matches.
Spurs had 61% possession, without dominating the territory inside the Dortmund third, and only managed one shot on target – Son’s second-half consolation goal.
But that only came because of a defensive mistake from away centre-back Neven Subotic, whose weak backpass was pounced on and punished by the South Korea international.
Aubameyang adds to growing reputation
Dortmund forward Aubameyang has become one of the hottest properties in European football, with Barcelona, Paris St-Germain and Manchester United reported to be eyeing a summer move for the 26-year-old.
And he enhanced his burgeoning reputation with two clinical finishes at White Hart Lane, taking his tally to 35 goals in all competitions this season.
Aubameyang provided a clinical edge for the visitors, who were defensively compact throughout and ready to spring forward at pace.
It resulted in Tottenham, who boast the meanest defence in the Premier League, being sliced open regularly and perhaps lucky not to lose by a wider margin.
Who can stop Dortmund?
Dortmund are bidding to become only the fifth club to win all three major Uefa trophies (European Cup/Champions League, Europa League/Uefa Cup and Cup Winners’ Cup) after Ajax, Bayern Munich, Juventus and Chelsea.
Based on their performance over the two legs against Spurs, few would bet against Thomas Tuchel’s side lifting the trophy in the Swiss city of Basel on 18 May.
One man who can help stop them is former manager Jurgen Klopp.
Klopp led the Bundesliga club to successive league titles in 2011 and 2012, as well as the 2013 Champions League final where they were beaten by Bayern Munich.
The pair, along with current holders Sevilla, will find out who they face in the quarter-finals when the draw is made at 12:00 GMT on Friday.
Man of the match – Pierre-Emerick Aubameyang (Dortmund)
What the managers said
Tottenham manager Mauricio Pochettino:
“I’m very disappointed we’re out of the Europa League but we need to recognise we played against a very good team who are playing at a Champions League level. Borussia Dortmund is one of the best teams in Europe.
“Tonight we showed we can compete at this level.
“I think we improved a lot, learned a lot from last week in Germany. We competed and we need to take positives.
“We have a lot of young players that need to feel what it means to compete in Europe and I think for the team it was a good test and we can take positive things.
Borussia Dortmund manager Thomas Tuchel:
“I think a 5-1 aggregate scoreline is a fair reflection and that makes me proud.
“We could have scored more in our home game, we were very dominant there, and we could have scored today even more with the transition game and the counter attacks.
“In the end it’s 5-1 and that means a lot for us, to beat Spurs, second in the Premier League, in both legs.”
Stats of the day
Spurs have scored in 19 consecutive home Europa League games (47 goals)
Son Heung-min has contributed seven goals for Spurs in the Europa League this season (three goals, four assists)
Pierre-Emerick Aubameyang has scored seven goals in eight Europa League games this season
Aubameyang has now been involved in 43 goals (35 goals, 8 assists) in 40 games for Borussia Dortmund in all competitions this season
Borussia Dortmund have progressed to the quarter-final of a European competition for the third time in four seasons, reaching the Champions League final in 2012-13 and the quarter-final in 2013-14