The final phase of the 1999–2000 UEFA Cup began on 23 November 1999 with the third round and concluded on 17 May 2000 with the final at the Parken Stadium in Copenhagen, Denmark. A total of 32 teams competed in this phase of the competition.
The third round included 24 winners from the second round and eight third-placed teams from the Champions League first group stage.
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Borussia Dortmund 2–2 Rangers on aggregate. Borussia Dortmund won 3–1 on penalties.----Juventus won 4–3 on aggregate.----Werder Bremen won 4–3 on aggregate.----Galatasaray won 3–2 on aggregate.----Lens won 5–3 on aggregate.----Parma won 5–4 on aggregate.----Slavia Prague won 5–2 on aggregate.----AS Monaco won 3–2 on aggregate.----Deportivo La Coruña won 5–3 on aggregate.----Bayer Leverkusen 2–2 Udinese on aggregate. Udinese won on away goals rule.----Arsenal won 6–3 on aggregate.----Leeds United 2–2 Spartak Moscow on aggregate. Leeds United won on away goals rule.----Roma won 1–0 on aggregate.----Celta Vigo won 8–1 on aggregate.----Atlético Madrid won 5–3 on aggregate.----Mallorca won 3–0 on aggregate.
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Udinese 2–2 Slavia Prague on aggregate. Slavia Prague won on away goals rule.----Galatasaray won 2–0 on aggregate.----Mallorca won 4–2 on aggregate.----Werder Bremen won 3–2 on aggregate.----Leeds United won 1–0 on aggregate.----Arsenal won 6–3 on aggregate.----Celta Vigo won 4–1 on aggregate.----Lens won 6–4 on aggregate.
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Leeds United won 4–2 on aggregate.----Galatasaray won 6–2 on aggregate.----Arsenal won 6–2 on aggregate.----Lens won 2–1 on aggregate.
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See also: 2000 UEFA Cup semi-final violence. ----
Arsenal won 3–1 on aggregate.----Galatasaray won 4–2 on aggregate.
See main article: 2000 UEFA Cup final.
The final was played on 17 May 2000 at the Parken Stadium in Copenhagen, Denmark.