This round saw the teams from UEFA's five highest ranked nations enter the fray, albeit to mixed results.
Getafe were made to work for their 3-1 success over Partizan Belgrade, scoring twice in three minutes at the very end to take a crucial lead to the Serbian capital.
The Spaniards were reduced to 10 men midway through the second half after Abdel Abqar was given his second yellow card of the match.
However, that did not stop them as substitute Andres Garcia netted the winner from close range three minutes from time. Johan Mojica then added a third a few moments later to give them an extra cushion.
This is Getafe's fourth season competing in Europe, having played group phase football in each of their previous three continental participations.
In Scotland, Freiburg battled back from an early setback to get past 10-man Motherwell 3-1. Regan Charles-Cook gave the hosts a lead less than five minutes in as The Steelmen look for their maiden appearance in a group stage.
But Freiburg, who made the Europa League final last May, turned things around. Matthias Ginter tied things up just before the half hour mark, before the centre-back converted a penalty after the break.
Keisuke Goto's third in stoppage time gave the Bundesliga outfit a more comfortable lead to take with them back to Germany.
Some of the top leagues' sides are left with more work to do. Brighton were held to a goalless draw in Norway against Tromso.
Despite having more than two-thirds of the possession and 25 shots on the road, the Seagulls could not find their way past a disciplined Tromso side.
Atalanta were also unable to find their way past Hapoel Tel Aviv as the Israelis held firm for a valuable 0-0 result in Bergamo.
AS Monaco secured a 3-2 victory at Gornik Zabrze, with Paris Brunner's goal 13 minutes after the break being the difference-maker for the Ligue 1 club.
Gornik have played in all three club competitions this summer, but will have to turn things around at Stade Louis II next week to avoid a triple elimination.
Borac, Larne near league phase return with away wins
In the domestic champion path, Northern Irish outfit Larne got the better of Lincoln Red Imps 2-0 on the road.
Playing up a man since the 29th minute, the away side created several chances in the second half before Paul O'Neill put them ahead six minutes from time.
Kevin O'Hara's stoppage time goal gives the Invermen a vital two-goal lead ahead of next week's decider.
Lincoln made the league phase last term, but were beaten at this stage of Conference League qualification two summers ago to Larne. On that occasion, they won the first leg before being defeated on their travels.
Borac Banja Luka were the other team in the champions path to prevail on Thursday, beating Vikingur Reykjavik 3-1. Two goals in two minutes midway through the first half had the Bosnians in a commanding spot in the match.
Vikingur, who beat Borac in the league phase in the 2024/25 season, got one back via a Gylfi Sigursson penalty towards the end, only to concede once more to see their seven-game winning streak in European home matches come to an end.
Drita took the lead twice against Andorra's Inter Club d'Escaldes, but they were unable to hold on as the latter claimed a 2-2 draw. It gives Inter a glorious chance to be their country's first-ever group phase participants, should they come out on top at home next week.
Shamrock Rovers led for most of the second half at home to KuPS Kuopio, but were pegged back in the 85th minute in a 1-1 stalemate. Both teams made the league phase last term, with the Finnish side going as far as the knockout play-offs.
KI Klaksvik and Riga FC played to a 0-0 tie in their game in the Faroe Islands. The Latvians are the other team in this path who have yet to play group stage football in Europe.
Greek sides held at home
Among the other main path matches, Greek clubs PAOK and Panathinaikos could only manage home draws.
The side from Thessaloniki needed an equaliser from Abdul Baba to cancel out Kristian Eriksen's opener for Brann in a 1-1 draw.
PAOK have reached the quarter-finals twice in the Conference League, and are the only Greek team to make the knockout stage of the competition on multiple occasions.
In Athens, Panathinaikos raced to a two-goal lead versus Hradec Kralove and were poised to take a lead with them to Czechia. That was before the visitors staged a late comeback to restore parity. Abdullahi Umar scored twice in the final moments as the match ended 2-2.
Both teams were in the knockout round of the Europa League in 2025/26, with Panathinaikos going a round farther.
Elsewhere, Ajax found their way past Sion 4-2 in Switzerland as the record Dutch champions scored all of their goals after the interval.
Should they complete the job in Amsterdam next week, de Godenzonen will qualify for the UECL group phase for the first time.
The other Dutch team in the round, Twente, were not as lucky, falling 1-0 to Qarabag at home.
Sporting Braga scored once in either half to top Austria Wien 2-0 at home. Pau Victor gave the Portuguese side the lead with a penalty, only to see his spot kick in the second half denied.
However, Braga did not panic, scoring a second goal near the end to have better control of the tie.
The match between Rapid Wien and Hearts ended 2-2 in Edinburgh as both sides took the lead in the contest. The result leaves the tie well-poised going into next Wednesday's decider.
Rangers edged Jablonec 1-0 at Ibrox despite playing the final stretch down a man.
As for FC Kobenhavn, they were unable to score in Finland against Inter Turku, who entered the competition in the first qualifying round. The 0-0 draw left the hosts the much happier of the two, with a potential upset being on the cards.
FC Midtjylland, FC Nordsjaelland, and FC Lugano all won their first legs, with the latter two clubs edge closer to a return to the competition's group phase.
For the exception of the Rapid vs Hearts tie, the return legs will be played next Thursday to decide the 24 teams that will qualify for the league phase. Joining them there will be the 12 losing sides from the Europa League play-off round.
Follow the final round of UEFA Conference League qualifying on Flashscore.