The German side threatened to run riot against the north Londoners, with the two goalscorers particularly impressive in a high-intensity performance from BVB.
Jurgen Klopp's men found themselves paired against the Premier League side for a third time in four seasons, having lost 1-0 at Signal Iduna Park last term and shared a 1-1 draw in 2011.
|VIEW FROM SIGNAL IDUNA PARK
|By Tom Maston
All over the place in defense, a lack of creativity and poor finishing - Arsene Wenger will have to answer some difficult questions following what really could have been a drubbing by Borussia Dortmund.
Ciro Immobile, Pierre Emerick-Aubameyang and Henrikh Mkhitaryan ran the Gunners ragged from the first minute, and only Wojciech Szczesny stopped things from becoming embarassing.
Things may have been different had Danny Welbeck converted a big chance at 0-0, but there are bigger issues that Wenger must address.
Italy international Immobile netted his first goal since he joined Dortmund from Torino with a superb solo effort, while Aubameyang's display of speed and incision punished Arsene Wenger's men again in the 48th minute.
Tellingly, Arsenal striker Danny Welbeck passed up good chances shortly before both Dortmund goals, but the scoreline was ultimately flattering to the England international and his teammates.
Former Manchester United playmaker Shinji Kagawa started on the bench following a goalscoring return to Dortmund colors against Freiburg on Saturday, while Sven Bender made his first appearance in midfield since February having recovered from a thigh injury.
Arsenal's defensive problems were well-documented before kickoff and, with Calum Chambers only among the substitutes due to a bout of tonsillitis, 19-year-old Hector Bellerin made his full debut at right back.
Mikel Arteta, starting in midfield due to Matthieu Flamini's thigh problem, had an early scare when Henrikh Mkhitaryan went down under his fifth-minute challenge but the Armenian was rightly booked for simulation.
Dortmund enjoyed the better of the opening exchanges but had to wait until the 27th minute for a clear opening, when Arsenal goalkeeper Wojciech Szczesny spread himself to deny Aubameyang on the end of Kevin Grosskreutz's cutback.
Two minutes later, Mkhitaryan blazed over under pressure from Jack Wilshere after Szczesny parried a low cross from Immobile.
Sebastian Kehl dispossessed the ineffective Alexis Sanchez and fed Aubameyang, whose tame 34th-minute finish allowed Szczesny to tip wide at the near post.
Welbeck spurned Arsenal's best opening of the half, shooting wide after Aaron Ramsey's deft pass got him in behind the Dortmund defense and the visitors were made to pay on the stroke of the interval.
Immobile stormed forward on the break from his own half and burst between Laurent Koscielny and Kieran Gibbs to arrow a clinical low finish across Szczesny.
Kehl made way for Matthias Ginter at halftime but it did nothing to disturb Dortmund's momentum as they once again tore forward with an intensity Arsenal's defense had no answer to.
Aubameyang forced the Premier League team to backpedal on this occasion and, although he stumbled in rounding Szczesny on the end of Grosskreutz's sumptuous return pass, he managed to steer a bouncing ball past Koscielny on the line.
Szczesny then tipped over a rasping Immobile strike as Dortmund threatened to run riot.
Welbeck could not turn home Gibbs' 57th-minute cross on a rare foray forward, which was was almost punished by Aubameyang - the 25-year-old's electric pace again reducing Arsenal to shreds as he found space to fizz a shot against the top of the crossbar.
Sluggish errors from Szczesny and Arteta were almost capitalized on by Aubameyang and Mkhitaryan as Arsenal's performance threatened to unravel completely.
As the clock ticked down on Wenger's first opening-day loss in the Champions League for 11 seasons, Welbeck turned cutely but blazed over to repeat another theme of the evening.
And the final whistle brought an end to a punishing experience for Arsenal, which will count itself lucky not to have suffered a heavier loss.