On 4 October 2008, Vukojević scored his first goal for Dynamo Kyiv, netting the opening goal in their 4–0 away win at Kharkiv in the Ukrainian Premier League. He went on to appear in all of Dynamo Kyiv's six UEFA Champions League group matches, helping the club to finish third in their group and continue their European campaign in the UEFA Cup. He continued to appear regularly in the competition and scored his first European goal for Dynamo Kyiv on 12 March 2009 in the first leg of their round of 16 tie against Metalist Kharkiv, netting the only goal in his team's 1–0 victory. He missed the second leg due to a yellow-card suspension as Dynamo won the tie on away goals and secured their place in the quarter-finals. During the quarter final second leg against Paris Saint Germain, he scored the final goal in a 3–0 win, helping the side to a 3–0 aggregate win.