The tie was finely poised ahead of the clash in the Slovakia capital after the two sides played out a 1-1 draw in Denmark last week. With home advantage in their favour, it was the hosts who started the second leg on the front foot, with Guram Kashia and Jamal Blackman both threatening before Marko Tolic broke the deadlock in the 33rd minute.
The 28-year-old received the ball on the right side of the box and neatly shifted it onto his left foot before stroking a low shot into the far corner.
After seeing his side strike first, Bratislava's goalkeeper Dominik Takac was quickly required to make a superb reaction save to keep out Darío Osorio’s close-range header.
Unfortunately for Takac, there was nothing he could do to prevent Aral Simsir from restoring parity just before the break. The Turkish attacker weaved through the Bratislava defence to create the space to drill a low shot past the despairing Takáč.
Buoyed from their equaliser, Midtjylland required just five second-half minutes to turn their game in their favour through Franculino’s exquisite volley. The Guinea-Bissau international showed great technique to hit Juninho’s lofted cross on the full, drilling the ball in off the post to net his third goal of the qualifying campaign.
As the clock drifted past the 70-minute, Franculino threatened to take the tie away from Bratislava, only to be denied by the resolute Takac.
Bratislava’s main draw dreams appeared to be fading until Marko Tolić produced a moment of magic in the 82nd minute. Similar to his first goal, Tolić rolled the ball onto his left foot and drove a powerful strike into the far corner. With momentum in their favour, the hosts went on to grab a dramatic winner through Tigran Barseghyan, who thumped a long-range shot into the bottom corner to fire the hosts into the main draw. As for the visitors, they will have to settle for a place in the UEFA Europa League for the third time in four seasons.
Flashcore Man of the Match: Marko Tolic (Slovan Bratislava)
Meanwhile, Lille saw off a valiant Slavia Prague to go through 3-2 on aggregate as the Czech side won 2-1 on the night - check out the report now.
Dinamo Zagreb and Red Star Belgrade also progressed with wins.
