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.
The draw mechanism for each round is as follows:
In the draw for the round of 32, matches were played between the winner of one group and the third-placed team of a different group, and between the runners-up of one group and the third-placed team from a Champions League group, with the group winner and runner-up host the second leg. Teams from the same national association or have played in the same group in the group stages cannot be drawn together.
From the round of 16 onwards, these restrictions did not apply, and teams from same group or same association could be drawn together.
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.
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.[1] The first legs were played on 18 February and 19 February, and the second leg matches were played on 26 February 2009.
Manchester City were the only team from the first qualifying round to reach the round of 16. 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 and Saint-Étienne reached the round of 16. Of the eight teams that entered the Round of the 32 from the UEFA Champions League group stage, two lost: Fiorentina and 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 and Paris Saint-Germain.
Dynamo Kyiv 3–3 Valencia on aggregate. Dynamo Kyiv won on away goals.
Round of 16
The draw for the round of 16 took place on 19 December 2008, immediately after the draw for the round of 32.[1] The first leg matches were played on 12 March, and the second leg matches were played on 18 March and 19 March 2009.
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.
Note: Between the 1999–2000 and 2008–09 seasons, the competition was still known as the UEFA Cup. All seasons are included following the competition's absorption of the Cup Winners' Cup.