Bruno Lage’s men took a mere six minutes to break the deadlock when Aston Villa loanee Enzo Barrenechea met Heorhiy Sudakov’s corner with a superb glancing header to score his first Benfica goal.
Sudakov was the provider once again 10 minutes later, threading in a superb ball to Vangelis Pavlidis to take into his stride and apply a clinical finish, capitalising on a horrible defensive mix-up involving Behlul Mustafazade and Kevin Medina.
Everything was adhering to the pre-match script until Portugal-born Leandro Andrade surprisingly halved the deficit. Marko Jankovic’s free-kick caused carnage in the Benfica box, and Andrade was on hand to rifle home a ferocious first-time strike.
The hosts were looking anything but comfortable, and almost had their lead wiped out when Kady Borges’ strike cannoned off the post, before Anatoliy Trubin made a fantastic save to deny Jankovic.
The Eagles headed into half-time feeling rattled, as Trubin was called into action again to deny Camilo Duran in added time.
That served as a warning sign of what was to come, and Duran completed an incredible turnaround when his brilliant angled finish clipped in off the post after the Colombian was expertly spotted by Jankovic.
Duran’s compatriot Richard Rios almost restored Benfica’s lead after being teed up by Andreas Schjelderup, but could only find the side netting with his close-range effort.
The Horsemen had the ball in the back of the net again through Mustafazade, but Benfica’s defensive blushes were spared by the linesman’s flag.
Lage’s side were struggling to reassert their early dominance on this clash, epitomised when Pavlidis’ long-range strike drifted harmlessly over the bar.
Gurban Gurbanov’s sat deeper in their shape heading into the closing stages, looking to hold onto a historic point.
But it was about to get even better for Azerbaijani champions, who completed arguably the finest comeback in their history when Abdellah Zoubir picked out Oleksiy Kashchuk, who fired home past Trubin.
Ultimately, Qarabag would hold on to claim all three points and dismiss any notion of being here to simply make up the numbers.
Meanwhile, this is a huge shock to the system for Benfica, who succumbed to a third defeat in their last 10 European matches (W5 D2) in the most dramatic of circumstances.
Flashscore Man of the Match: Camilo Duran (Qarabag)