The Premier League club went down 2-1 to Fenerbahçe 2-1 at home but they had to take cover from the fireworks thrown by the Turkish fans before advancing thanks to a 3-0 victory in Istanbul last Thursday.
The unsavoury scenes happened right at the start of the play-off second leg at the City Ground and there is likely to be UEFA action.
Kerem Akturkoglu's goal midway through the first half and his penalty early in the second were not enough for the Turks as Callum Hudson-Odoi earned a 4-2 win on aggregate.
VfB Stuttgart also confirmed their spot in the Europa League last 16 despite a 1-0 home loss to Celtic, their 4-1 victory in Glasgow last week proving crucial.
Ferencváros, Lille, Panathinaikos, Bologna, Genk and Celta Vigo are also in the hat for Friday's draw. Genk drew 3-3 at home with Dinamo Zagreb to advance 6-4 on aggregate.
In Stuttgart, Luke McCowan confidently scored in the first minute for Celtic but the hosts dominated from there on. The first-leg cushion meant the Germans cruised to a 4-2 aggregate victory.
Sebastian Hoeness' side had two goals ruled out for video review offsides and striker Deniz Undav told RTL: "The most important thing is to go through, the rest doesn't matter.
"VAR should actually be there to help. It feels like it makes more wrong decisions than the referees themselves. It's getting funnier and funnier."
Stuttgart will play Porto or fellow Portuguese side Braga on March 12 and 19, with the exact pairings to be decided in Friday's draw.
Robbie Keane's Ferencváros turned around their first-leg deficit with a 2-0 home victory over Ludogorets setting up a 3-2 aggregate win.
Gabi Kanichowsky and Norwegian Kristoffer Zachariassen, continuing a memorable week from his nation in European football, netted in the first half for the Hungarian outfit.
Lille prevailed 2-0 at Red Star Belgrade after extra-time to go through 2-1 on aggregate. Olivier Giroud headed in early in normal time to make up for last week's surprise home defeat and substitute Nathan Ngoy clinched their last 16 place on 99 minutes.
Rafa Benitez's Panathinaikos beat Viktoria Plzen 4-3 on penalties to advance despite having substitute Javi sent off in extra-time.
The game in the Czech Republic ended 1-1 in normal time after Andreas Tetteh scored from the edge of the box for his third goal across both legs for the Greeks.
Karel Spacil equalised with a strong header before a goalless extra 30 minutes left the tie at 3-3 on aggregate.
Bologna beat Brann 1-0 in Italy to ease through 2-0 overall. The Norwegians had Jacob Sørensen dismissed in the first half for a foul.
Celta won 1-0 at home to PAOK, adding to their 2-1 victory in Thessaloniki last week.
In the Conference League, Fiorentina fought back from 3-0 down at home to Poland's Jagiellonia Bialystok as two extra-time goals sealed their passage to the 16 despite a 4-2 defeat on the night.
Crystal Palace also advanced from Thursday's play-off second legs with Celje, Samsunspor, Rijeka and Sigma Olomouc. AZ Alkmaar and Lech Poznan beat Noah 4-1 and KuPS Kuopio 3-0 on aggregate respectively.
The second leg in Florence was expected to be a stroll given Fiorentina's 3-0 win in the first leg. However, the Serie A strugglers were forced into extra-time following Bartosz Mazurek's hat-trick.
The Italians risked joining Champions League flops Inter and Juventus in going out of Europe this week, but Nicolò Fagioli's stunner lit up the Stadio Artemio Franchi before Taras Romanczuk's own goal.
Palace beat Zrinjski Mostar 2-0 with goals from Maxence Lacroix (36th) and Evann Guessand (93rd) for a 3-1 win on aggregate.
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