Qarabag were held to a goalless draw by Inter Milan on Thursday and missed out on becoming the first Azerbaijani side to progress to the last 32 of the Europa League.
The hosts thought they had secured a match-winning strike deep in injury time when Richard Almeida's shot took a deflection and beat Inter goalkeeper Juan Pablo Carrizo only for the referee to disallow it for offside.
Dnipro leapfrogged Qarabag into second place with a 1-0 triumph over St Etienne in the other pool game, allowing the Ukrainian outfit to join Inter in the next round of the competition.
Qarabag finished third in the pool, two points adrift of Dnipro.
Italian giants Inter, having already sealed their progression as Group F winners, carried an unbeaten record to Azerbaijan for the final pool game.
Inter coach Roberto Mancini made wholesale changes to the side that lost 2-1 to Udinese in Serie A on Sunday with no player that started at the weekend included in the line-up to face Qarabag.
Neither teams took a shot on goal until the 39th minute when Dani Osvaldo fed Federico Bonazzoli just outside the area and his left-footed strike towards the far post was kept out by Qarabag goalkeeper Ibrahim Sehic.
Qarabag coach Gurban Gurbanov was forced to make his first substitution shortly after with Namiq Yusifov replacing an injured Vuqar Nadirov in attack.
The hosts had a good chance to go in front before half-time.
Muarem Muarem spotted Leroy George in the box and his 10-yard effort was saved by Carrizo.
Qarabag kept up the pressure and 10 minutes into the second half, Muarem fed George in the area and his diagonal shot was saved by Carrizo.
At the other end, Ibrahima Mbaye's header from Joel Obi's cross went over the bar.
With 15 minutes remaining, and Qarabag needing a win to remain alive in the competition, George drilled a left-footed strike from 30 yards that was kept out by Carrizo.
The home side never gave up and for a moment thought they had sealed a place in the next phase but Almeida's shot was ruled out by the assistant.