Only two teams were able to overturn first leg deficits in Thursday's play. Viktoria Plzen had the more impressive comeback, taking down Crvena zvezda 5-1 after extra time in Czechia.
After losing the first leg 3-0 last week, the hosts grabbed an early goal, only to be pegged back minutes later. Plzen, who have not been eliminated from a Europa League qualifying tie since 2020/21, received three penalties in the second half in a chaotic 45 minutes.
Prince Adu had his kick saved, before Denis Visinky netted his effort. Between the two penalties, Red Star were reduced to 10 men. Christophe Kabongo netted his effort from the spot to make 4-4 on aggregate. Plzen made the most of their man advantage in extra time, as David Krcik scored the winner to help them overcome their heavy first leg loss.
Zvezda will play in the Conference League for the very first time after losing consecutive two-legged ties in Europe. That has not occurred since 2016/17, the season they missed out on group phase football.
Omonia Nicosia were the other team to turn things around, edging Sint-Truiden 4-3 over the two legs after a 4-2 victory in the decider.
The Cypriot side were propelled by a Lois Diony hat-trick, with Nikolas Panagiotou adding a fourth near the end to put the match beyond reach. STVV's maiden European journey will continue in the UECL after a best-ever third-place finish in Belgium last term.
Ferencvaros are back in the Europa League proper after finishing off Trabzonspor 4-0 in Budapest. Playing up a man from the 13th minute on, and two men up for the final 33 minutes, the Hungarian champions ran away with the game, getting three of their goals after the break.
Fradi successfully negotiated all four rounds of UEL qualification this summer, winning six of the eight matches while drawing the other two.
It was the third straight two-legged tie that Trabzonspor have failed to progress from.
RB Salzburg's 10th Europa League group phase participation was confirmed after a 3-0 victory over debutants Mjallby. That completed a 4-0 aggregate success for the Austrians. Anderlecht also came out on top in both legs of their tie, topping Kairat Almaty 3-0 for the second week running.
Benfica's Gianluca Prestianni scored twice in a 3-1 defeat of AGF Aarhus, matching their result from last week's first leg.
As Aguias ended a run of four European away matches without victory en route to qualifying for the group phase six years on from their last showing.
Ararat-Armenia strike late
Armenia are the latest country to have a first-ever participant in the UEL proper after Ararat-Armenia edged CS Universitatea Craiova 1-0, winning 2-1 overall.
Despite being outshot 22-5, the home side ending up handing their Romanian opponents a sucker punch at the death. Sandro Lima's initial penalty was denied, but the Brazilian followed up from close range to send the home fans into delirium.
Ararat-Armenia were twice knocked out of the UEL at this stage of the competition, back in 2019/20 and 2020/21.
Egnatia were close to a memorable result, but conceded late on versus Lillestrom in a match that would ultimately go to extra time. The Norwegians grabbed their winner four minutes in before holding on for a 2-1 victory on the night and on aggregate.
Another debutant in the Europa League main rounds, Jagiellonia Bialystok finished off Iberia 1999 with a 2-1 win in Georgia to complete a 6-1 aggregate success.
Fellow Polish side Lech Poznan also advanced following their 2-2 draw at FC Thun, completing a 9-2 victory overall. It will be their first appearance back in the group phase since 2020/21.
Thun are the second Swiss team to participate in the group stage or league phase of all three major UEFA club competitions after Basel.
One of the most unexpected results on Thursday occurred in Lithuania, where Kauno Zalgiris earned an impressive 1-0 result over Besiktas.
While Renan Oliveira's goal shortly past the hour mark was not enough to help the hosts progressed - they were beaten 3-1 across the two legs - the single result alone was their best win in European play.
OFI Crete got past CSKA Sofia 2-0 on the road, meaning they advance 5-0 on aggregate. Goals in either half saw the Greek Cup winners prevail.
The league phase draw will take place on Friday, with the 12 sides that advanced from the play-off round joining 11 eliminated teams from the Champions League, as well as 13 direct entrants. The first of eight matchdays will begin on 16 September.
Follow the UEFA Europa League on Flashscore as the competition returns in September.