Hertha BSC Berlin struck late to beat FC Ameri Tblisi while FC Basel 1893 and Olympique de Marseille edged their Central-East ties on away goals.
FC Ameri Tbilisi 2-2 Hertha BSC Berlin (agg: 2-3)
Ameri gave themselves hope of an upset by twice taking the lead but the German outfit cancelled out both efforts to progress to the next stage, Solomon Okoronkwo's first-leg winner proving to be the difference between the two sides. The hosts began the game well and captain Georgi Davitnidze tapped the ball in from close range following an 18th-minute corner. Ameri could ill-afford to concede a goal on home soil but they did so on 35 minutes when Brazilian international Gilberto eluded two defenders before laying the ball off for Srdjan Lakić who made no mistake. Early in the second half Suliko Davitashvili scored from two metres out following another corner but Hertha's Marko Pantelić finished off a lively move by the visitors seven minutes from time to seal the tie.
Olympique de Marseille 0–0 BSC Young Boys (agg: 3-3, Marseille win on away goals)
One goal would have been enough for the Swiss side to progress and it almost came in the last seconds of added time when Hakan Yakin's free-kick found Steve Gohouri, who fed Marcos Dos Santos and he headed against the crossbar. Marseille had the majority of the other chances but their three away goals in the first leg proved enough to carry them through as the score remained blank in France.
Wisła Kraków 1–0 SV Mattersburg (agg: 2-1)
Polish league runners-up Wisła progressed at the expense of their visitors from Austria after a narrow victory. A goal by striker Piotr Brożek was the difference between the sides on the night as he converted a cross from left winger Marek Zienczuk on 23 minutes. The home side dominated and found the net again through Brazilian forward Jean Paulista on 61 minutes but his effort was ruled out by an offside flag. Mattersburg midfielder Michael Michael Mörz was sent off for a second yellow card on 86 minutes and, after the final whistle, his team-mate Christian Fuchs was also dismissed.
FC Dinamo Minsk 2–3 FC Artmedia (agg: 3-5)
Artmedia killed off resistance from the Belarussian side after weathering an early storm. Leonid Kovel forced Artmedia's Ľuboš Kamenár into a fine early save but Juraj Halenár hit them on the counterattack with a 31st-minute strike and Vratislav Gajdoš doubled their advantage seven minutes later. Peter Burák added a third for Artmedia on 62 minutes although Kovel and Marcio subsequently scored to give Dinamo Minsk some consolation.
FC Sion 1–0 SV Ried (agg: 1-0)
Sion overcame their Austrian rivals thanks to a penalty from former Ried player Sanel Kuljić. Herwig Drechsel had hit the post for Ried with a tremendous shot before a penalty was awarded for goalkeeper Michael Mehlem's foul on Gelson Fernandes. The keeper was dismissed and his replacement Thomas Gebauer could not block Kuljić's spot-kick on 35 minutes. Sion failed to press their advantage further in the second half but weathered a late storm to progress.
Grasshopper-Club 2-0 FC Fehérvár (agg: 3-1)
Krassimir Balakov's side took their Hungarian opponents by storm to seize a place in the first round. The 20-year-old Scott Sutter put Grasshoppers ahead after just five minutes as they made an aggressive start and they put the tie beyond Fehérvár midway through the first half as midfielder Antonio dos Santos scored a second. The Zurich side sat back to defend after the interval but were rarely troubled.
SK Slavia Praha 0–0 FK Karvan Evlakh (agg: 2-0)
Slavia dominated possession but were unable to capitalise despite creating a host of opportunities. They wasted two major chances within the opening ten minutes when Martin Latka had a header cleared off the line by Gocha Trapaidze and Stanislav Vlček shot wide in a one-on-one situation against goalkeeper Elkhan Hasanov.
Wisła Plock 1–1 FC Chornomorets Odesa (agg: 1-1, Chornomorets win on away goals)
Serhiy Shyshchenko's first-half goal proved to be crucial as the Ukrainian side progressed on away goals. Paweł Sobczak had hit the post for Polish Cup winners Plock before Shyshchenko exploited a 31st-minute defensive error to beat goalkeeper Robert Gubiec. Speedy winger Wahan Geworgyan converted Czech team-mate Tomáš Došek's cross after 62 minutes but Plock could not find a winning goal.
FC Vaduz 2-1 FC Basel 1893 (agg: 2-2, Basel win on away goals)
Basel found it difficult squeeze past as they needed an away goal by Zdravko Kuzmanovic to progress. Juan Mauel Sara and Marco Ritzberger scored for the hosts as a crowd of 3,600 enjoyed the match between the Liechtenstein team and their neighbours from Switzerland. Kuzmanovic scored with his head from a rebound to equalise on the night and ultimately secure Basel's passage.
FC Metalurh Zaporizya 3-0 CSF Zimbru Chisinau (agg: 3-0)
F.Y.R. Macedonia forward Darko Tasevski scored twice as Zaporizhya recorded a convincing 3-0 victory. The visitors took the lead after 16 minutes when Tasevski played a one-two with Serhiy Silyuk before sending a low shot under Nicolae Calancea. Nine minutes after the restart, the 22-year-old struck again as he capped a mesmerising solo run with a crisp finish and, 20 minutes from time, David Kvirkvelia put the result beyond doubt when he pounced on a rebound.
FC BATE Borisov 0–2 FC Rubin Kazan (agg: 0-5)
Rubin completed a comfortable 5-0 aggregate victory thanks to two goals from Alejandro Dominguez. Under-strength BATE managed to hold their guests at bay for 35 minutes until a thunderous drive from the Argentinian playmaker broke their resistance. He scored a second on the counterattack nine minutes later. BATE tried to raise their game and had a goal disallowed for offside in the second half.