The 2008–09 season saw a setback when Boenisch suffered an injury ahead of a new season. He became a regular in the first team and spent the most of the season in the left-back position, competing the position with Petri Pasanen. Boenisch then made his UEFA Champions League debut, making his first start, in a 0–0 draw against Cypriot side Anorthosis Famagusta. In a match against Borussia Dortmund on 18 October 2008, Boenisch provided two of the three goals in a 3–3 draw. Despite suffering from injuries, Boenisch, who played all nine UEFA Cup league matches, played the whole 120 minutes of the game and was booked for dissent in the 2009 UEFA Cup Final to level the game at 1–1, however his team went on to lose the game 2–1 to Shakhtar Donetsk after extra time. Nevertheless, the club would win the DFB-Pokal after beating Bayer Leverkusen 1–0; this was Boenisch's first title in his career.