Dortmund led 2-0 from the first leg but were on the back foot from the opening whistle, with Atalanta neutralising the visitors' advantage by half-time thanks to goals from Gianluca Scamacca and Davide Zappacosta.

Mario Pasalic gave the hosts the lead in the tie but Karim Adeyemi's solo effort dragged Dortmund level.

With the match set for extra time, Ramy Bensebaini was penalised for catching Nikola Krstovic in the face with a high boot in the box.

Referee Jose Sanchez duly pointed to the spot and handed Bensebaini a second yellow card.

Samardzic blasted home the penalty in the 98th minute with virtually the last kick of the match.

Atalanta's former Arsenal defender Sead Kolasinac said he went through "a whirlwind of emotions" in the final seconds.

"When the referee decided for a penalty, I didn't know who would take it. All our penalty takers had been substituted, but luckily Lazar converted brilliantly," Kolasinac told DAZN.

Atalanta will meet either Premier League leaders Arsenal or German champions Bayern Munich in the last 16, with the draw to be held on Friday.

The victory and qualification continues Atalanta's resurgence under Raffaele Palladino, who took over from the struggling Ivan Juric in November.

Under Palladino, Atalanta are unbeaten domestically in 10 matches in 2026.

The victory also helped save the blushes of Italy's Champions League sides in this season's competition.

Inter Milan's surprise elimination to Bodo/Glimt on Tuesday left Atalanta and Juventus, who host Galatasaray later on Wednesday trailing 5-2 from the first leg, as the only remaining Serie A sides in the competition.

Not since 1987-88 had a Serie A club failed to make it to the last 16 of the European Cup.

Floored by their earliest Champions League exit since 2021-22, 2024 finalists Dortmund will need to pick up the pieces quickly with Bundesliga leaders Bayern Munich set to visit on Saturday.

Dortmund captain Emre Can told DAZN that his error-prone side deserved their elimination.

"If you make so many individual errors, it's going to be difficult to progress... We were very unlucky, but to be honest we didn't deserve to advance."

- Dortmund's hopes "50-50" -

Despite their first-leg advantage, Dortmund coach Niko Kovac had said on Monday that his side's chances of reaching the last 16 were "50-50" and promised not to sit back and defend their first-leg lead.

Visiting goalkeeper Gregor Kobel saved a Nicola Zalewski effort with four minutes gone but Atalanta broke through a minute later when Scamacca tucked home with ease from close range after Bensebaini's failed clearance.

Dortmund were stung again just before half-time when Zappacosta's speculative attempt took a heavy deflection off Bensebaini and went in.

With Dortmund's first-leg lead eroded, Atalanta continued to turn the screw. Pasalic headed in a Marten de Roon cross early in the second half to grab the lead in the tie.

Substitute Adeyemi levelled the aggregate score when he curled in a superb effort from the edge of the box with 15 minutes left.

With extra-time beckoning, Bensebaini's nightmare evening got even worse as he connected with Krstovic's head late in stoppage time.

Despite him touching the ball first, VAR found the contact to be dangerous with the Algerian given his marching orders and Sanchez pointing to the spot.

Serbian midfielder Samardzic held his composure to slam home the penalty left-footed.