Qarabag scored a dramatic stoppage-time winner to end Eintracht Frankfurt's hopes of reaching the Champions League play-offs and keep their own alive.
Behlul Mustafazade became the first Azerbaijani player to score in the competition with the last kick of a topsy-turvy contest, with the result leaving the hosts 19th in the table on 10 points and almost certainly guaranteeing their spot in the play-offs.
Eintracht Frankfurt, who are now eliminated, have collected a meagre four points from seven matches and sit 33rd.
The Germans arrived in Azerbaijan having dismissed head coach Dino Toppmoller on Sunday after just one win in nine games.
And they made the worst possible start when Colombia forward Camilo Duran scored the first of his two goals for Qarabag inside four minutes.
But Frankfurt, who host Tottenham in their final match, responded via Can Uzun and a second-half penalty from Fares Chaibi before their defensive frailties were exposed again.
For the second time in the evening a marauding run from Elvin Cafarquliyev laid on a goal for Duran, before Mustafazade delivered the knockout blow and took the pressure off their trip to Liverpool on 28 January.
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