Roma reached the last 16 of the Europa League, while German sides Bayer Leverkusen and Wolfsburg also booked their places after Thursday's early action.
Roma, 1-0 winners against Gent in the first leg, looked in danger when Jonathan David levelled the tie on aggregate after 25 minutes but Justin Kluivert eased the Serie A side's nerves with a quick equaliser that earned a 2-1 overall victory.
Inter Milan also secured passage to the next stage, though an empty San Siro was the eerie backdrop for their 2-1 win over Bulgarian side Ludogorets that sealed a 4-1 triumph on aggregate.
The lockdown of one of football's most famous stadia had followed the coronavirus outbreak in the region, leading to the visiting players wearing facemasks upon their arrival in Italy.
On the pitch, Cauly Oliveira Souza hauled Ludogorets back into the tie in the 25th minute but an own goal from Georgi Terziev six minutes later restored Inter's two-goal cushion, before Romelu Lukaku clinched the win just before the break in bizarre fashion - a diving header coming off the goalkeeper and back off his head.
While Roma and Inter made it through, Ajax were eliminated after suffering a 3-2 aggregate defeat to Getafe, for whom Jaime Mata scored a crucial away goal early on. The Liga side held on after Danilo and Carel Eiting had offered up hope for the Dutch giants.
Elsewhere, Leverkusen blew Porto away with a 3-1 win in Portugal to triumph 5-2 on aggregate.
Lucas Alario, Kerem Demirbay and Kai Havertz scored to seal a comfortable second-leg victory, before Moussa Marega grabbed a consolation for the home side.
Another Bundesliga side, Vfl Wolfsburg, saw off Swedish side Malmo 3-0 away - Josip Brekalo, Yannick Gerhardt
and Joao Victor on target - to breeze through 5-1 on aggregate.
FC Basel also sailed through with a 1-0 home win over APOEL Nicosia courtesy of Fabian Frei's penalty that secured a 4-0 aggregate victory against the Cypriots.
Sporting exited after losing 4-1 at Istanbul Basaksehir after extra time to go down 5-4 on aggregate after Edin Visca gave the hosts a lifeline with a late goal in normal time and then scored a penalty to take them through to the last 16.
Fellow Portuguese side Benfica are also out following a 3-3 home draw and 5-4 aggregate loss to Shakhtar Donetsk, with Alan Patrick scoring the all-important third goal for the visitors 11 minutes from time.
LASK Linz upset visiting Dutch side AZ Alkmaar 2-0 with a Marko Raguz double which gave the Austrians a 3-1 aggregate success.
Sevilla endured a goalless draw at home to CFR Cluj to claim a last-16 place by away goal following a 1-1 draw in the first leg.
Joy for Wolves, Man Utd but Celtic, Arsenal crash
Wolves took a 4-0 advantage to Espanyol and despite a last-gasp 3-2 defeat in Spain, that first-leg damage proved decisive.
Adama Traore scrambled in a close-range effort and Matt Doherty also scored as Wolves twice cancelled out goals by Jonathan Calleri, who got a hat-trick in a 3-2 home win that restored some pride for the Liga side.
Rangers had become the first side through when they edged Braga 1-0 on Wednesday to seal a 4-2 aggregate victory.
But Celtic failed to join their Scottish Premiership rivals in the hat after they suffered a 4-2 aggregate defeat to Copenhagen.
Following a 1-1 draw in the first leg, the Danes took the lead early in the second half at Celtic Park through Michael Santos, only for Odsonne Edouard to haul the Bhoys level from the penalty spot with seven minutes remaining.
With the game poised for extra time, Copenhagen silenced the partisan home crowd with two goals in the dying minutes from Pep Biel and Dame N'Doye.
Arsenal also crashed out after suffering late heartbreak in their last-32 tie with Olympiakos.
Holding a slender 1-0 advantage from the first leg in Greece, Pape Abou Cisse forced extra time with a 53rd-minute header at the Emirates Stadium.
With the game closing in on a penalty shoot-out, Pierre-Emerick Aubameyang put Mikel Artetta's side 2-1 up on aggregate on the night with a goal in the 113th minute, only for Youssef El-Arabi's 23rd goal of the season in the dying moments to send last year's beaten finalists out on away goals.
In stark contrast, Manchester United crushed Club Brugge 5-0 at Old Trafford to ease into the last 16.
United's 6-1 aggregate win was sparked by the 22nd-minute dismissal of Simon Deli for a clear handball, although there was still a VAR review, resulting in Bruno Fernandes converting the penalty.
Fernandes was involved when Juan Mata teed up Odion Ighalo for a goal on his full debut seven minutes later, with Scott McTominay making it 3-0 before the break, and Brazilian midfielder Fred wrapping up the rout with a late brace for
only his second and third goals since a £53m move from Shakhtar Donetsk in June 2018.
Last-16 line-up to be completed on Friday
Strong winds forced the postponement of Salzburg's second leg at home to Eintracht Frankfurt. The match will now be played on Friday night, with the hosts looking to overturn a 4-1 deficit.