Sevilla lost 4-3 at Slavia Prague after conceding a last-minute goal in extra time to go out 6-5 on aggregate, while Eintracht Frankfurt beat Inter 1-0 to advance. At the Emirates Stadium, Aubameyang celebrated his second goal by pulling on a Black Panther mask he had placed behind the advertising boards, after coming to the rescue for an Arsenal side that lost the first leg 3-1 in France last week.
The Gunners erased that deficit in just 15 minutes, with Aubameyang scoring early and then setting up Ainsley Maitland-Niles for the second, before adding his second in the 72nd. Another favorite, Benfica, needed extra time to advance, eliminating Dinamo Zagreb 3-1 on aggregate.
Chelsea had the most comfortable evening, and biggest victory, as Olivier Giroud celebrated his 50th European game by scoring a hat trick in a 5-0 rout of Dynamo Kiev. Marcos Alonso and Callum Hudson-Odoi also had one apiece for Chelsea.
Elsewhere, Napoli advanced 4-3 on aggregate against last year's semifinalist Salzburg despite losing the second leg 3-1. Valencia advanced thanks to an injury-time goal from substitute Goncalo Guedes that secured a 1-1 draw at Krasnodar and a 3-2 aggregate victory, while Villarreal eliminated Zenit St. Petersburg 5-2 on aggregate.
Here's a look at Thursday's action:
The biggest drama took place in Prague, where Slavia came from a goal down in extra time as substitute Peter Olayinka scored the winner in the 199th minute.
Slavia led twice in regulation but Sevilla came back both times for a second straight 2-2 draw between the sides that forced extra time. Franco Vazquez then put the Spanish side ahead with a header in the 98th minute, but Slavia equalized just four minutes later through Mick van Buren.
In regulation, Michael Ngadeu-Ngadjui and Tomas Soucek scored for Slavia, while Wissam Ben Yedder and Munir El Haddadi replied for Sevilla.
Ben Yedder's goal came from a penalty in the 44th, while Soucek also converted from the spot in the 47th.
It was a flying start for Arsenal.
Aubameyang opened the scoring five minutes into the game after tapping in a cross from Aaron Ramsey. Just 10 minutes later, Aubameyang contributed again, this time crossing for Maitland-Niles to head in the second. However, replays showed that the striker was offside before delivering the cross.
Aubameyang sealed the win with another easy tap-in when he met Henrikh Mkhitaryan's cross, and immediately ran to grab his Black Panther mask before pulling it over his head. It was the latest superhero of choice for the Gabon international, who has previously pulled on Batman and Spider-Man masks after scoring while playing for Borussia Dortmund.
"In Gabon, we call the national team the Panthers of Gabon, so it represents me," Aubameyang said.
GIROUD ON TARGET
Giroud made sure Chelsea was in control from the start.
He netted in the fifth minute from close range after a corner kick from Willian landed right in front of him. Coach Maurizio Sarri didn't have striker Gonzalo Higuain available because of an illness, but Giroud was more than an adequate replacement.
He added his second in 33rd after Alonso set him up with a cross from the left. And in the last move of the first half, Giroud released Hudson-Odoi free on the left to cross for Alonso who tapped in the third.
In the 59th, Giroud rose in the area to head in Willian's free kick from the right for his ninth goal in nine Europa League matches to top the scoring table.
Giroud also set up Hudson-Odoi's final goal.
Napoli coach Carlo Ancelotti had to swallow his first loss in the Europa League after winning the previous three games, but it was still enough to advance.
Napoli striker Arkadiusz Milik opened the scoring with a volley 14 minutes into the game, putting the overall result beyond doubt. Milik also scored in the 3-0 victory in the first leg last week.
Munas Dabbur answered that one for Salzburg later in the first half for his eight. Substitutes Fredrik Gulbrandsen and Christoph Leitgeb completed the comeback in the second half.
Substitute forward Jonas scored for Benfica in the 71st minute, four minutes after coming off the bench, to erase Zagreb's 1-0 advantage from the first leg and take the game to extra time. Francisco Ferreira and Alex Grimaldo then scored to complete the comeback for Benfica.
In Milan, Luka Jovic lobbed Inter goalkeeper Samir Handanovic early for Frankfurt to advance 1-0 on aggregate after the two played to a goalless draw in Frankfurt in the first leg.
Gerard Moreno and Carlos Bacca scored in each half to guide Villarreal to a 2-1 home win. Branislav Ivanovic got a consolation goal for the visitors.
After losing the first leg 2-1 in Spain, Krasnodar looked set to advance on the away goals rule after Magomed Suleymanov gave it a 1-0 lead five minutes from time. But Guedes secured a spot in the last eight for Valencia in the third minute of injury time.
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