The 2008–09 FC Basel season began off with various pre-season matches against Swiss lower league teams, as well as against German Bundesliga, Ukrainian Vyscha Liha and Polish Ekstraklasa clubs.

To prepare for the 2008–09 season, FCB added defenders Behrang Safari from Malmö FF and David Abraham from Gimnàstic de Tarragona and midfielders Jurgen Gjasula and Marcos Gelabert from FC St. Gallen.

In the other direction, fans' favourite Daniel Majstorović left the club for AEK Athens, while Kōji Nakata returned to Japan with Kashima Antlers; Vratislav Lokvenc and David Degen's respective loan deals were not re-newed.

Basel played their opening game of the season in Bern on 18 July 2008 against Young Boys, which they won 2–1 through goals by substitutes Marko Perović and Benjamin Huggel after Eudis had put the home side ahead.

Basel head coach Christian Gross gave most of his regular rest, including goalkeeper and captain Franco Costanzo and played with a reserve team.

After a few chances, in the 14th minute Marko Perović put in a hard cross so close to the near post that goalkeeper Chassot couldn't help but knock the ball over the goal line.

After a foul on Streller in the 66th minute referee Cyril Zimmermann awarded a penalty for Basel, which Benjamin Huggel converted on the top right-hand corner.

Likewise Basel had nothing to show for their late pressure as David Abraham, Gjasula and Huggel failed to net the ball with their chances, the end score remained 1–1.

Göteborg started into the game fastest and having come close to scoring within a few seconds, they soon had the goal that they needed to remain in the fixture as in the 19th minute Pontus Wernbloom finished off a fast counterattack.

This shook Basel to life and Benjamin Huggel, the man who put them ahead last week in Gothenburg, managed the same feat again as he headed in a Jürgen Gjasula corner.

The only player who was added to Basel's starting lineup compared to the first leg was Valentin Stocker and he nearly scored the home team's second, but Göteborg's goalkeeper Kim Christensen was able to smother the effort.

Having already played five league games and the first two qualifiers, Basel had quickly found their rhythm and attempted to force the pace from the beginning, both Valentin Stocker and Ivan Ergić went close to goal in the opening minutes of the first half.

With a neat pass coming from Basel's Portuguese midfielder Carlitos who set up the chance for his team-mate, but Stocker fired left footed just beyond the post.

The home team were unable to outwit the stubborn and hard Basel defence, not even after coach Manuel Cajuda brought in two new strikers in an attempt to strengthen the attacking force in the second half.

Basel created good opportunities through Marcos Gelabert and Eren Derdiyok and even if they had more possession and even if they were the stronger attacking team for the rest of the half, their efforts were all in vain because the hard-working Guimarães defence held tight.

Because they were a goal behind, Guimarães were forced to do the pressing, but as they equalised for a second time, through substitute Roberto Calmon Félix with just three minutes left, he was ruled offside by referee Pieter Vink and his linesman.

Barça were one of the favorites to win the trophy, and Basel had bad memories of the Sporting team, who had knocked them out of the 2007–08 UEFA Cup knockout stage this year in February.

Basel central defender François Marque with a clumsy challenge on Luiz Adriano about thirty metres out, allowed the deep-lying playmaker Fernandinho another chance.

Basel left-back Ronny Hodel was overwhelmed by the speed of the break and Luiz Adriano ran clear of him into the open space and passed to Brandão in the box.

Abraham attempted to clear under pressure struck the ball hard, but it hit Reto Zanni and looped back behind goalkeeper Franco Costanzo into the net.

Head coach Gross took out Eduardo Rubio after the break, he brought Valentin Stocker, but within 60 seconds of the restart Costanzo was beaten again as Krkić finished off a quick played counterattack with his hard shot.

Home team coach Josep Guardiola left Lionel Messi, Xavi and Samuel Eto'o on the bench and, therefore, much was expected from Andrés Iniesta and, luckily for Barça he was on form on the day, ready to run and with a good eye.

Barça missed another opportunity to take the lead before half-time, as Sylvinho delivered a free-kick which Henry met with a header in towards the top corner of the goal but Costanzo matched this chance too.

Again, after the break the Argentinian keeper confirmed his credits as Henry passed the ball into space in front of Bojan Krkić, who was able to run clear, but Costanzo was able to block the chance with his feet.

Due to the absence of centre-back Dmytro Chyhrynskyi and right-winger Ilsinho through injury, plus suspended striker Brandão, home coach Mircea Lucescu had to make changes in his team.

Five minutes into the second half, Willian doubled the score, coming from the left-hand touchline, swerved around several defenders before arching the ball inside the far post, despite Costanzo's desperate dive.

A measured ball found Yannick Djaló racing clear, and though his cross was met by a powerful header from the again unmarked Derlei, Franco Costanzo parried this.

Ivan Ergić did find the target soon after, but his drive lacked sufficient power to trouble goalkeeper Tiago, while Djaló may have scored a second, had his stand foot not slipped after he had cleverly created space inside the box.

The half-time introduction of Valentin Stocker gave Basel increased power down the left wing and, seconds after the restart, an early cross from him led to Marco Streller shooting wide of the goal.

Fabien Frei eventually brought a save out of Tiago with a low drive 16 minutes from time, while Stocker forced the goalkeeper into two stops in quick succession.