The 2008–09 season saw Shakhtar win the Super Cup and the UEFA Cup. On 15 July 2008, Shakhtar emerged victorious in the Super Cup Final against Dynamo Kyiv. At the end of extra time, the teams were level at 1–1. In the ensuing penalty shoot-out, Shakhtar converted all five of its penalties to win 5–3. Srna, who captained the side, scored one of the penalties. On 3 August, he scored the first goal in a 3–0 victory over Illichivets Mariupol. On 13 August, he scored the first goal in a 2–0 victory over Dinamo Zagreb in the Champions League. On 18 October he scored a goal in Shakhtar's 4–2 win against Kryvbas. On 2 March, he scored the winning goal in Shakhtar's 2–1 league victory over Illichivets. On 22 March, he scored the only goal in a league win over Vorskla. In the semi-final of the UEFA Cup, Shakhtar faced Dynamo Kyiv in an all-Ukrainian tie. After a 1–1 away draw in the first leg, Shakhtar won 2–1 at the Donbass Arena for a 3–2 aggregate win to progress to the final. Darijo played the full 90 minutes of both legs. On 20 May 2009, he captained Shakhtar in the 2–1 victory over Werder Bremen in the UEFA Cup Final. Srna provided the assist for Jádson's winning goal seven minutes into extra time. He also picked up a yellow card. This was the last UEFA Cup before its rebranding as the UEFA Europa League. Shakhtar finished the Premier League season in second position, 15 points behind champions Dynamo Kyiv. Darijo made 46 appearances and scored 5 goals, with 25 appearances and 4 goals in the league.