The Armenia international set up goals for Marco Reus and Pierre-Emerick Aubameyang as the Azerbaijan outfit proved no match for Thomas Tuchel side
The 26-year-old set up Marco Reus to open the scoring in the 28th minute, the winger collecting his team-mate’s pass before unleashing a long-range effort that found the back of the net.
Mkhitaryan then assisted BVB’s second when he sent Pierre-Emerick Aubameyang through on goal, allowing the club top-scorer to finish with ease.
The contest was as good as over when Sergey Zenjov put the ball past his own goalkeeper, before Mkhitaryan deservedly got his name on the scoresheet when he crashed his drive in off the underside of the crossbar three minutes later.
With Krasnodar defeating PAOK 2-1 in Group C’s other fixture on Thursday, three points were enough to book Thomas Tuchel’s outfit a spot in the knockout stages.
The hosts controlled the early exchanges and Dawid Pietrzkiewicz almost gifted the home side a goal in the 11th minute, only for Mkhitaryan to let him off the hook by volleying over from his poor clearance.
The Qabala keeper was more assured five minutes later when he stayed big to stop Aubameyang netting the opener following a sprint down the right, with Gonzalo Castro sending the follow-up wide.
After almost fumbling a deflected Matthias Ginter strike into his own net, Pietrzkiewicz was finally beaten after 28 minutes when Reus fired a low shot past him from the edge of the box – making it 31 successive games in which Dortmund have scored.
The hosts grew in confidence and a ferocious 20-yard drive from Aubameyang flew narrowly wide before a last-ditch block from Rafael stopped Reus – who pulled up with a groin issue after celebrating his goal – from scoring his second nine minutes prior to the interval.
Pietrzkiewicz produced a great save to keep out Mkhitaryan in the final minute of the half, but moments later he let Aubameyang’s stabbed effort from the left-hand side of the box slip past him as Tuchel’s side doubled their advantage.
Adnan Januzaj replaced Reus at the interval but Dortmund remained dangerous, with Mkhitaryan steering Marcel Schmelzer’s low cross onto the upright.
Pietrzkiewicz went some way to redeeming himself midway through the second half when he thwarted Januzaj, but from the resultant corner Zenjov headed the ball into his own net.
Mkhitaryan finally got in on the scoring act 20 minutes from time, slamming home from 18 yards after being fed by Lukasz Piszczek.
The Armenia international came close to adding a fifth, but his 74th-minute strike crashed off the post before rebounding off the Qabala keeper and going wide.