Braga knocked out Chievo, as Eintracht Frankfurt and Auxerre secured progression.
Wenderson Wender's extra time strike saw Sporting Braga progress past Chievo and into the Uefa Cup group stage, despite the Portuguese side tasting defeat on the night in Verona.
With Braga having registered a 2-0 lead in the first leg, the onus was on the Serie A outfit and they received encouragement through Simone Tiribocchi's 37th minute effort.
And Denis Godeas's goal 20 minutes from time saw the tie all square and heading for extra time.
Wender's strike shortly before half time in extra time proved crucial as it gave the Portuguese team the all-important away goal.
Italian frustrations boiled over, and Andrea Zanchetta received his marching orders at the restart of extra time.
Eintracht Frankfurt secured progression after negating the threat of Brondby with a 2-2 draw in Denmark.
Leading 4-0 from the first leg, the Bundesliga outfit had already done the hard work, but there was no complacent approach from the visitors as Aleksander Vasoski shot his side into the lead inside six minutes.
Martin Ericsson restored parity on the night in the 19th minute, but seven minutes after half time, Macedonia international Vasoski struck again.
Thomas Rasmussen levelled just after the hour to restore some pride for the hosts, but Eintracht saw out the final half an hour comfortably enough to progress 6-2 on aggregate.
Ireneusz Jelen scored twice as Auxerre claimed a comfortable passage past Dinamo Zagreb.
The Ligue 1 outfit claimed a 3-1 win and 5-2 aggregate success with Jelen (35 & 42) getting the ball rolling for his side.
A penalty from Da Silva Eduardo in the 61st minute gave a glimmer of light to the visitors, but Lionel Mathis (70) made sure of the win.
Partizan Belgrade advanced despite suffering defeat at Groningen.
With Partizan holding a 4-2 lead from the first leg, the tie was finely balanced and the Dutch outfit would have fancied their chances.
And even more so after Koen Van Der Laak's successful conversion of a penalty on the hour. But, with the hosts requiring just one more goal to secure an away goals win, their late pressure failed to bear fruit.
Goals from Carsten Ramelow (76) and a penalty from Bernd Schneider (86) rescued Bayer Leverkusen from a potential cup upset at the hands of FC Sion.
After a goalless draw in Switzerland in the first leg, Andrei Voronin gave the hosts the lead in the 62nd minute.
Voronin's strike was cancelled out by Fernandes Gelson just 10 minutes later, however, as the visitors claimed an away goals lead in the tie.
But that advantage lasted a matter of seconds as Ramelow struck, and then Schneider put the seal on the win.
Hapoel Tel Aviv progressed past Ukrainian side Chornomorets 4-1 on aggregate following a 3-1 victory on Thursday.
Salim Toama got the ball rolling for the Israelis in the 24th minute, and Elyaniv Barda effectively settled the tie midway through the second half.
To their credit, Chornomorets refused to wilt and pulled a goal back nine minutes from time through Gennadi Nizhegorodov. But Luciano De Bruno put the seal on a comfortable win for the hosts in the 88th minute.
Already leading 3-0 from the first leg, Heerenveen advanced past Vitoria Setubal of Portugal following a goalless draw at Abe Lenstra Stadion.
A brace of goals from Fernando Baiano and one from Fabian Canobbio saw Celta Vigo beat Standard Liege 3-0, to progress 4-0 on aggregate.
Claudiu Niculescu scored twice as Dinamo Bucharest claimed a 4-1 win over Greek side Xanthi and progression to the next stage courtesy of an 8-4 aggregate win.
Niculescu struck first in the 11th minute, and Adrian Cristea doubled his side's lead on the night two minutes after the interval.
The visitors pulled a goal back in the 51st minute through Jacques Paviot, but Xanthi faced an uphill task in attempting to stem the tide of the tie.
Ionel Danciulescu regained his side's two-goal lead in the 79th minute, and two minutes later Niculescu bagged a fourth.
Espanyol defeated Artmedia Bratislava 3-1 to progress 5-3 on aggregate.
Jan Buryan gave the Slovakian visitors a 14th minute lead and a 3-2 advantage overall.
But Walter Pandiani (19) and Ferran Coro (66) turned the tie in the Liga side's favour and Pandiani put the icing on the cake in the 80th minute.
Extra time goals from Mert Nobre and Deivison Bobo secured Besiktas progression the hard way after CSKA Sofia's 2-0 win in normal time in Bulgaria.
With the Turks having claimed a 2-0 lead in the first leg, Besiktas started the second leg in pole position, but CSKA had other ideas.
Valentin Iliev hauled his side back into contention on the hour and nine minutes later Aleksandar Tunchev doubled his side's lead and restored parity in the tie overall.
Extra time followed, but within three minutes of the restart, Nobre had notched to secure a crucial away goal, and the tie was effectively settled by Bobo in the 97th minute.
Czech side Slovan Liberec, meanwhile, completed a memorable 4-2 aggregate win over Crvena Zvezda.
Already leading 2-1 from their home leg, Liberec matched that result with an impressive win in Yugoslavia.
The writing was on the wall for the hosts, perhaps, as early as the first minute when Jiri Bilek put the visitors into an instant lead.
Goncalves Ailton hauled his side level two minutes before half time, but Liberec confirmed their win via Jan Holenda in the 65th minute.
An 89th minute strike by Bosko Balaban handed Club Brugge a 2-1 aggregate victory over SCP Ruzomberok of Slovakia.
The Belgians held a one-goal lead from the first leg, but that advantage was cancelled out by Robert Rak in the 28th minute.
The tie appeared poised for extra time until former Aston Villa striker Balaban's late intervention.
Grasshoppers secured a resounding 5-0 win and progression past Swedish side Atvidaberg.
Having secured a 3-0 victory in the first leg, the Swiss side were always in control and made sure of victory - goals from David Blumer and Scott Sutter either side of the half hour mark made the aggregate score 5-0 and the second half a mere formality.
And three goals from Roland Schwegler, Ribeiro Eduardo and Michel Renggli within 10 second half minutes completed the 8-0 aggregate rout.
A goalless draw at De Kuip was just enough for Feyenoord to claim an away goals victory over Lokomotiv Sofia - following a 2-2 first leg draw in Bulgaria.
A double from Markus Rosenberg helped Ajax to a 4-0 victory over Start and completed the Dutch side's 9-2 aggregate romp.
Rosenberg struck in the sixth and 25th minutes and Zdenek Grygera claimed his side's third goal two minutes before half time. Ryan Babel completed the scoring in the 68th minute.
Elsewhere, Roman Wallner's 65th minute strike gave Austria Vienna a 1-0 win over Legia Warsaw and a 2-1 aggregate victory.
Uefa Cup first round, second leg (aggregate score in brackets):
Ajax 4-0 IK Start (9-2)
Austria Vienna 1-0 Legia Warsaw (2-1)
Auxerre 3-1 Dinamo Zagreb (5-2)
Bayer Leverkusen 3-1 FC Sion (3-1)
Brondby 2-2 Eintracht Frankfurt (2-6)
Celta Vigo 3-0 Standard Liege (4-0)
Chievo 2-1 Braga (2-3)
Club Brugge 1-1 Ruzomberok (2-1)
Crvena Zvezda 1-2 Slovan Liberec (2-4)
CSKA Sofia 2-2 (AET) Besiktas (2-4)
Dinamo Bucharest 4-1 Xanthi (8-4)
Espanyol 3-1 Artmedia Bratislava (5-3)
Feyenoord 0-0 Lokomotiv Sofia (2-2 Feyenoord through on away goals)
Grasshoppers 5-0 Atvidabergs FF (8-0)
Groningen 1-0 Partizan Belgrade (3-4)
Hapoel Tel-Aviv 3-1 Chornomorets (4-1)
Heerenveen 0-0 Vitoria Setubal (3-0)
