The knockout stage of the 2008–09 UEFA Cup began on 18 February 2009, and concluded with the final at the Şükrü Saracoğlu Stadium in Istanbul on 20 May 2009. The final phase involved the 24 teams that finished in the top three in each group in the group stage and the eight teams that finished in third place in the UEFA Champions League group stage. Each tie in the final phase, apart from the final, was played over two legs, with each team playing one leg at home. The team that had the higher aggregate score over the two legs progressed to the next round. In the event that aggregate scores finished level, the team that scored more goals away from home over the two legs progressed. If away goals are also equal, 30 minutes of extra time were played. If goals were scored during extra time and the aggregate score was still level, the visiting team qualified by virtue of more away goals scored. If no goals were scored during extra time, there would be a penalty shootout after extra time.

<section begin=Format /> The draw mechanism for each round is as follows: In the final, the tie was played over just one leg at a neutral venue. If scores were level at the end of normal time in the final, extra time was played, followed by penalties if scores had remained tied. # [Willian assists Fernandinho to score for Shakhtar Donetsk | upload.wikimedia.org/wikipedia/commons/d/db/UEFA///Cup///Semifinal///in///Kiev///%28DK///vs///SD%29///130.jpg]

Bracket

Round of 32

<section begin=R32 /> The draw for the round of 32 took place on 19 December 2008, the day after the final round of UEFA Cup group stage matches. The first legs were played on 18 February and 19 February, and the second leg matches were played on 26 February 2009. [Manchester City](https://bliptext.com/articles/manchester-city-f-c) were the only team from the first qualifying round to reach the round of 16. [Braga](https://bliptext.com/articles/s-c-braga) were the only team from the Intertoto Cup to reach the round of 16 and were therefore awarded the title of Intertoto Cup winners. Of the eight teams who had been placed in Pot 5 of the group stage draw, only [Metalist Kharkiv](https://bliptext.com/articles/fc-metalist-kharkiv) and [Saint-Étienne](https://bliptext.com/articles/as-saint-tienne) reached the round of 16. Of the eight teams that entered the Round of the 32 from the [UEFA Champions League group stage](https://bliptext.com/articles/2008-09-uefa-champions-league-group-stage), two lost: [Fiorentina](https://bliptext.com/articles/acf-fiorentina) and [Bordeaux](https://bliptext.com/articles/fc-girondins-de-bordeaux). Of the eight ties between a third-placed team and a first-placed team from the UEFA Cup group stage, two were won by the third-placed team; the winners were [Braga](https://bliptext.com/articles/s-c-braga) and [Paris Saint-Germain](https://bliptext.com/articles/paris-saint-germain-fc). <section end=R32 />

First leg

Second leg

CSKA Moscow won 3–1 on aggregate. Metalist Kharkiv won 3–0 on aggregate. Hamburger SV won 4–0 on aggregate. ''Marseille 1–1 Twente on aggregate. Marseille won 7–6 on penalties.'' Paris Saint-Germain won 5–1 on aggregate. Galatasaray won 4–3 on aggregate. Zenit St. Petersburg won 4–2 on aggregate. ''Werder Bremen 3–3 Milan on aggregate. Werder Bremen won on away goals.'' Braga won 4–1 on aggregate. Udinese won 4–3 on aggregate. Manchester City won 4–3 on aggregate. Ajax won 2–1 on aggregate. Saint-Étienne won 5–2 on aggregate. Aalborg BK won 6–1 on aggregate. Shakhtar Donetsk won 3–1 on aggregate. ''Dynamo Kyiv 3–3 Valencia on aggregate. Dynamo Kyiv won on away goals.''

Round of 16

<section begin=R16 /> The draw for the round of 16 took place on 19 December 2008, immediately after the draw for the round of 32. The first leg matches were played on 12 March, and the second leg matches were played on 18 March and 19 March 2009. <section end=R16 />

First leg

Second leg

Werder Bremen won 3–2 on aggregate. Marseille won 4–3 on aggregate. ''Metalist Kharkiv 3–3 Dynamo Kyiv on aggregate. Dynamo Kyiv won on away goals.'' Shakhtar Donetsk won 2–1 on aggregate. Udinese won 2–1 on aggregate. Hamburger SV won 4–3 on aggregate. ''Manchester City 2–2 Aalborg BK on aggregate. Manchester City won 4–3 on penalties.'' Paris Saint-Germain won 1–0 on aggregate.

Quarter-finals

<section begin=QF /> The draw for the quarter-finals took place on 20 March 2009. The first legs were played on 9 April and the second legs were played on 16 April. <section end=QF />

First leg

Second leg

Hamburger SV won 4–3 on aggregate. Dynamo Kyiv won 3–0 on aggregate. Shaktar Donetsk won 4–1 on aggregate. Werder Bremen won 6–4 on aggregate.

Semi-finals

<section begin=SF /> The draw for the semi-finals took place on 20 March 2009, immediately after the draw for the quarter-finals. The first legs were played on 30 April and the second legs on 7 May. <section end=SF />

First leg

Second leg

Shakhtar Donetsk won 3–2 on aggregate. ''Werder Bremen 3–3 Hamburger SV on aggregate. Werder Bremen won on away goals.''

Final

<section begin=F /> The final was played on 20 May 2009 at the [Şükrü Saracoğlu Stadium](https://bliptext.com/articles/kr-saraco-lu-stadium) in [Istanbul](https://bliptext.com/articles/istanbul), Turkey. <section end=F />