Die Werkself were required to come from two goals down to rescue a 2-2 draw in the first leg, setting up an intriguing return fixture in Germany with a quarter-final spot up for grabs.
Match preview
Leverkusen's record-breaking unbeaten run in all competitions was in serious danger of coming to an end last week, as Qarabag entered the final 20 minutes of the first leg in Azerbaijan with a two-goal lead thanks to first-half strikes from Yassine Benzia and Juninho.
However, Xabi Alonso - who made eight changes to his starting lineup - had to rely on a couple of substitutes to restore parity for Die Werkself, with Florian Wirtz initially pulling one back with a fine run and finish before Patrik Schick headed home a dramatic 92nd-minute equaliser.
Leverkusen followed up just their fifth draw of the campaign with their 31st victory in all tournaments when they beat 10-man Wolfsburg 2-0 in the Bundesliga last Sunday. Nathan Tella and Wirtz found the net either side of half time after Mortiz Jenz's early dismissal to maintain the club's 10-point lead at the summit with just nine games remaining.
After losing out to Roma in the Europa League semi-finals last season, Leverkusen are determined to go one better this term and reach their first European final since the 2001-02 Champions League showpiece event. Die Werkself should be confident of success on Thursday as they have progressed from seven of the 10 previous European knockout ties after drawing the first leg.
Leverkusen will welcome a return to the BayArena where they have won all three games in the Europa League this season, including a thumping 5-1 group-stage win over Qarabag in October. Alonso's men are bidding to become only the second team in UEFA Cup/Europa League history to score four or more goals in four consecutive home games after themselves back in 1994-95.
Competing in the last 16 of a major European competition for the first time in their history, Qarabag certainly did themselves proud in the first leg, with Leverkusen boss Alonso admitting after the match that the Azerbaijani side "were unlucky" to not hold on for a famous triumph.
The Horsemen have since extended their unbeaten run in all competitions to eight games after beating Zira 3-1 on home soil last weekend - their 14th win in their last 15 Azerbaijan Premier League matches.
Goals from Nariman Axundzada, Richard Almeida and Adama Diakhaby helped Qarabag register their 20th top-flight success of the campaign and preserve their whopping 23-point lead at the summit, and they now require just eight points from their final 10 matches to win a third title in a row.
Gurban Gurbanov's side have had few problems finding the net this season, as they have scored at least twice in each of their last five Europa League matches, while they have only failed to score in one of their last 17 games in UEFA competition.
Making the net ripple again may not be enough for Qarabag come out on top on Thursday, though, as they have lost all four of their previous visits to Germany, while their only defeat in their last six Europa League away games was the aforementioned 5-1 loss at Leverkusen earlier this season.
Bayer Leverkusen Europa League form:
W
W
W
W
W
D
Bayer Leverkusen form (all competitions):
W
W
W
W
D
W
Qarabag FK Europa League form:
L
D
W
W
L
D
Team News
Leverkusen duo Victor Boniface and Artur remain sidelined with respective groin and thigh injuries, while backup goalkeeper Matej Kovar has emerged as a doubt after missing last weekend's game with a muscle problem; first-choice shot-stopper Lukas Hradecky could be called upon to start his first Europa League game of the campaign.
Jeremie Frimpong served a domestic suspension last weekend, but he is available for selection on Thursday and is set to battle with Tella and Josip Stanisic for a start at right wing-back, while Alex Grimaldo continues on the left.
Only Pierre-Emerick Aubameyang (10) and Romelu Lukaku (eight) have contributed to more Europa League goals than Wirtz (seven - three goals and four assist) so far this season, and the highly-rated German is expected to operate in the number 10 role, with or instead of Amine Adli as Schick competes with Borja Iglesias for a start up front.
As for Qarabag, they will be boosted by the return of left-back Elvin Cafarquliyev and midfielder Julio Romao, who are both expected to start after missing the first leg through suspension.
Cafarquliyev could join Marko Vesovic, Bahlul Mustafazada and Badavi Guseynov in the back four, protecting former Leverkusen goalkeeper Andrey Lunev.
Romao and Marko Jankovic are the most likely duo to link arms in centre-midfield as Leandro Andrade, Benzia and Abdellah Zoubir all provide support in attack for central striker Juninho, who has scored three of his four Europa League goals this season away from home.
Bayer Leverkusen possible starting lineup:
Hradecky; Kossounou, Tah, Tapsoba; Frimpong, Palacios, Xhaka, Grimaldo; Adli, Wirtz; Schick
Qarabag FK possible starting lineup:
Lunyov; Vesovic, Mustafazada, Guseynov, Cafarquliyev; Romao, Jankovic; L. Andrade, Benzia, Zoubir; Juninho
We say: Bayer Leverkusen 3-1 Qarabag FK (Bayer Leverkusen to win 5-3 on aggregate)
Alonso may not be so tempted to makes mass changes to his Leverkusen lineup this time around and should turn to some of his star names from the off in a bid to take control of proceedings and begin the second leg in better fashion than the first.