Looking to recover from the 1-0 first leg deficit, Aberdeen boss Stephen Glass made just the one change from the side that drew 1-1 at Hearts on Sunday. With Connor McLennan injured, Jack MacKenzie returned to the side at left-back, Jonny Hayes moving further up the pitch as a result.
For Qarabag, with Patrick Andrade suspended, Ismayil Ibrahimli deputised in midfield in the only change to the side that featured in the first leg in Baku.
In a crackling Pittodrie atmosphere, Aberdeen were quick out of the blocks, Calvin Ramsay and Funso Ojo combining well down the right to cause some early alarm in the Qarabag defence in the first minute.
Ramsay was the source again on five minutes, a deep cross to the back post reaching Ramirez whose header back across goal was cleared by Medvedev. The Dons were certainly wound up for the game and looking to tear into their opponents.
But from nowhere, on eight minutes Qarabag were ahead. Zoubir pulled the ball back from the by-line and, coming onto it on the corner of the six yard box, Bayramov ripped a shot across the face of goal and into the far corner for 1-0.
Aberdeen responded immediately and good work between Lewis Ferguson and Ojo won a 10th minute corner, Magomedailyev clutching Ramsay's cross.
Kady was inches away from doubling the lead on 11 minutes, Medvedev playing the ball into Hüseynov on the left edge of the box. He slid a pass through the six yard box which, fortunately, just eluded Kady's finishing touch.
Kady didn't miss on 18 minutes though. Ross McCrorie gave the ball away in midfield and the visitors worked it back into Zoubir around the edge of the box. Holding onto the ball, he waited his moment and fed the unmarked Kady at inside-right and he slotted the ball in first time, albeit looking suspiciously offside as he did so.
It might have been worse on 23, Zoubir twisting and turning into the box and, looking ready to pull the trigger, Scott Brown appeared to take the ball of his toe.
Ramsay put in another corner on 25 minutes leading to a scramble at the back post, the ball eventually ricocheting behind off Brown. Qarabag were adamant there should have been a free-kick given, Kady booked for his protests. On the break from that goal-kick, Sheydaev was in behind, Joe Lewis making a sharp save from a tight angle.
The visitors then had a spell of one corner after another down their right, but they came to nothing. MacKenzie became the first Aberdeen man booked on 32 minutes for a challenge on Romero.
The Dons finally had Qarabag on the back foot again on 38 minutes, Hayes accelerating away down the left and firing in a dangerous looking cross, Magomedailyev grabbing the ball at full stretch as Christian Ramirez lurked behind him.
Another Qarabag break on 43 minutes almost had Sheydaev in again, but his attempted lob was plucked out of the air by Lewis, limiting the damage of a disappointing first half for the home team.
HALF-TIME: ABERDEEN 0 QARABAG 2
Jay Emmanuel-Thomas replaced Teddy Jenks at the break as the Dons went chasing the three second half goals they needed to rescue the tie.
Ibrahimli was in the book within a minute of the restart, scything down Ojo. The free-kick from the right caused problems for the Qarabag 'keeper, but his defenders were ultimately able to work it clear.
Frustration again on 51 minutes, a great pass out from MacKenzie eluding Medina, but as Ojo looked to be in on goal the ball just held up and Qarabag were able to bundle the ball clear. A low cross from Ferguson two minutes later looked dangerous but Magomedailyev was down sharply to smother again.
Ojo hauled down Kady as he looked to get Qarabag on the break on 58 minutes and he was the second Aberdeen man to be cautioned. Ferguson joined him two minutes later.
Hayes was close to pulling one back on 61 minutes, cutting inside from the right, curling a left foot shot across goal, the goalkeeper punching the ball behind. From Ramsay's corner McCrorie was up at the back post but he was always stretching and headed wide. Qarabag were swiftly on the break shortly after, Brown hauling Zoubir down and getting a yellow card.
Emmanuel-Thomas took a quick free-kick on 66 minutes, a clever piece of thinking that caught Qarabag cold. Ramirez got in behind, but under pressure from a defender, his shot flew wide.
The tie was emphatically finished on 72 minutes when Zoubir smashed in a vicious drive from 20 yards. He was played in from the centre circle by Kady, receiving the ball on the edge of the box, showing good feet and then burying the ball into the bottom corner.
Qarabag made their first change on 74 minutes, Ozobic replacing Kady. While he was settling in, Ramsay fired in a corner to the near post, Ferguson hooking the ball over the bar. Niall McGinn then replaced Hayes.
Ojo looked to reduce the arrears on 76 minutes, his drive from 18 yards flying over the goalkeeper and landing on the roof of the net. Emmanuel-Thomas was next with a pot shot on 79 minutes, Magomedailyev seeing it all the way into his gloves.
Sheydaev and Romero were replaced for Qarabag on 81 minutes by Gurbanli and Vesovic while the Dons brought on Dean Campbell for Ramirez who had taken a knock on the thigh a few minutes earlier. Garayev and Medina were the next to make way, Almeida and Mustafazade coming on for them as the game ebbed towards its conclusion.
As the game entered time added on, Ramsay was flattened by Almeida on the edge of the box, giving the Dons a late penalty. Ferguson stepped up and smashed in a late consolation, sending the 'keeper the wrong way. It meant nothing in the context of the game, but it was some reward for 90 minutes of genuine, honest effort against a side that, frankly, looks too good for the Conference League.