Salihamidžić was limited to just 29 appearances for the 2005–06 season, but made 42 seasonal appearances in his final season with the club, in which he also scored five goals. One of Salihamidžić's most memorable plays in 2006–07 was in the Champions League round of 16 second leg against Real Madrid, where he dispossessed Roberto Carlos and fed the pass to Roy Makaay, who beat goalkeeper Iker Casillas and set the record for the fastest goal in tournament history, at 11 seconds after kickoff. This helped Bayern overcome a 3–2 loss from the first leg to level the tie at 2–1 and advance on the away goals rule.