Pizarro's role was fundamental in the qualification of Werder Bremen to the UEFA Cup Final, scoring a goal in the 3–2 away victory over Hamburg on 7 May, completing a 3–3 aggregate victory over their German rivals in the semi-finals. However, with the absence of playmaker Diego in the final against Shakhtar Donetsk, Pizarro could not save the team from a 2–1 defeat after extra time to the Ukrainian champions on 20 May 2009 at the Şükrü Saracoğlu Stadium in Istanbul.