Thursday's biggest result came in Latvia, where Auda completed a massive upset in defeating FCSB 4-1 in their return leg. Barthelemy Diedhiou scored twice for the hosts, who already led 3-2 from the first match.
Joao Paulo had tied the game just before the hour mark, reducing FCSB's deficit back down to one, but it all went downhill after that for the Romanians, who conceded three more times in the final quarter of the game to suffer an unexpected elimination.
It is the second time that Auda will compete in the Conference League third qualifying round, having done so two years prior. They will fancy their chances against Albania's Dinamo Tirana, who knocked off Aluminij 3-0 in their match, advancing 4-1 over the two legs.
Auda are joined by Riga FC - who won their tie earlier in the week - as well as RFS in the next round. RFS had eliminated Vestri 5-2 on aggregate despite their 1-1 draw in Iceland.
Inter Turku also pulled off a memorable result, beating Istanbul Basaksehir 2-0 to knock out the Turkish club 3-1 over two legs. It marks the second time ever that the Finnish club have reached the third qualifying round in a UEFA club competition.
Ludogorets were also unable to shake off their loss from last week against Hapeol Tel Aviv. The Bulgarian team, who had won 14 straight domestic titles before being dethroned last term, drew 2-2 in their home leg to lose 4-2 overall.
Having missed a penalty in the first half, the side from Razgrad had scored twice in seven second half minutes to go within one of their Israeli opponents, but Emmanuel Boateng restored the two-goal lead shortly thereafter which helped send his team through.
It is the first time since 2015/16 in which Ludogorets will not feature in a group stage/league phase in Europe.
Cyprus' AEK Larnaca were on the wrong side of an early exit at the hands of Israeli opposition following a penalty shootout reverse to Beiter Jerusalem.
They had forced extra time thanks to a stoppage time leveller to win 3-2 in the second leg, having lost 1-0 in the opener. Yet, AEK failed to convert two of their final three kicks to fall 4-3 in the shootout.
Beitar are in the third qualifying round for the second year running, having lost at that stage in 2025.
Some of the more favoured sides also made it through. That included Ajax, who came from a goal down to top Vojvodina 4-1 for the second week running, as well as Sporting Braga during their 4-0 defeat of Zeljeznicar Pancevo. That saw the Portuguese side through 5-0 on aggregate.
It was not as simple for Panathinaikos though, who held off Paksi 2-2 at home, which proved to be enough as the Greek club advanced 4-3 in total. Gent were pushed all the way to penalties versus LNZ Cherkasy after another 0-0 stalemate, but the Belgians did go through in the end with a 4-2 win from the spot.
Zalgiris score seven in remarkable comeback
Through all of the chaos of Thursday, the match with the most goals was in Lithuania. Zalgiris Vilnius, having lost 3-0 away to Dinamo Tbilisi last week, had their work cut out for them in their home leg.
Yet, the former UECL group stage participants did not give up. Although they failed to put away a penalty, Zaliai Balti still found a way to turn things around. They never went behind in the match, scoring thrice in the final eight minutes - including a winner in the 88th minute - to win 7-2 on home soil.
Zalgiris have only scored seven goals once in a two-legged tie, having done so in two games in the 1994/95 UEFA Cup Winners Cup.
Fellow Lithuanian side Panevezys were not so lucky though, losing on penalties to Tobol Kostanay after a 1-1 second leg kept the tie level.
Flora Tallinn also went the distance in their match against The New Saints where the Welsh side scored in stoppage time to make it 1-1 on aggregate (1-0 on the night). It remained that way throughout extra time, befroe the Estonian outfit held their nerve in the shootout to prevail 4-2.
Other teams in the domestic champions path to advance include ML Vitebsk, Gyor, and Borac Banja Luka. The club from Belarus were the only ones to win on the day, scoring late to beat Sutjeska 2-1 to complete a 5-1 success across the two legs.
Sutjeska's loss meant that the four Montenegrin sides in Europe this term lost all 10 of their matches combined.
Rijeka got past Derry City 1-0 for the second week in a row, while fellow Croatian club Varazdin were not as lucky, failing to hold onto their first leg advantage against Jablonec in a 2-0 reverse in Czechia and 3-2 aggregate loss.
Nordsjaelland impressed in a 6-0 drubbing of GAIS to overturn their defeat a week prior. The Danes moved on 6-1 overall. As for Hibernian, they recovered from their shock loss in Kosovo versus Malisheva to prevail 4-1 on the night and 4-3 on aggregate. They and fellow Scottish side Motherwell - 3-0 winners over HB Torshavn to win 5-0 over two legs - are through.
The third qualifying round will occur over the next two weeks and will feature 60 teams: 52 in the main path, and eight in the champions path. The 30 winning teams will advance to the play-off round at the end of August.
Keep up to date with all of the UEFA Conference League action on Flashscore.