The final phase of the 2000–01 UEFA Cup began on 21 November 2000 with the third round and concluded on 16 May 2001 with the final at the Westfalenstadion in Dortmund, Germany. A total of 32 teams competed in this phase of the competition.
The third round included 24 winners from the second round as well as 8 third placed teams from the Champions League first group stage.
| Seeded teams | Group | Unseeded teams | ||
|---|---|---|---|---|
| Team | Coefficient rating | Team | Coefficient rating | |
| 103.799 | 1 | 43.433 | ||
| 56.562 | 32.525 | |||
| 48.201 | 32.250 | |||
| 46.201 | 8.062 | |||
| 79.964 | 2 | 42.201 | ||
| 60.333 | 32.201 | |||
| 51.050 | 29.799 | |||
| 46.364 | 14.500 | |||
| 78.964 | 3 | 43.201 | ||
| 64.364 | 29.201 | |||
| 53.799 | 24.433 | |||
| 52.333 | 15.583 | |||
| 65.964 | 4 | 45.433 | ||
| 61.275 | 34.799 | |||
| 49.728 | 14.562 | |||
| 48.638 | 29.799 | |||
|}
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Internazionale win 2–1 on aggregate.----Parma win 4–2 on aggregate.----VfB Stuttgart win 4–3 on aggregate.----Rayo Vallecano win 2–0 on aggregate.----PSV Eindhoven win 4–0 on aggregate.----Roma win 4–0 on aggregate.----Nantes win 7–4 on aggregate.----Bordeaux win 4–1 on aggregate.----
Liverpool win 4–2 on aggregate.----AEK Athens win 6–4 on aggregate.----Celta Vigo win 1–0 on aggregate.----Alavés win 4–2 on aggregate.----Porto win 2–0 on aggregate.----Slavia Prague win 5–3 on aggregate.----Barcelona win 3–1 on aggregate.----1. FC Kaiserslautern win 3–1 on aggregate.
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1. FC Kaiserslautern won 1–0 on aggregate.----Celta Vigo won 2–1 on aggregate.----PSV 4–4 Parma on aggregate. PSV won on away goals rule.----Barcelona won 6–0 on aggregate.----Deportivo Alavés won 5–3 on aggregate.----Porto won 4–3 on aggregate.----Rayo Vallecano won 6–2 on aggregate.---- Liverpool won 2–1 on aggregate.
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Barcelona 4–4 Celta Vigo on aggregate. Barcelona won on away goals rule.----Liverpool won 2–0 on aggregate----Alavés won 4–2 on aggregate----Match interrupted for 16 minutes due to supporter disturbances.
1. FC Kaiserslautern won 2–0 on aggregate
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Alavés won 9–2 on aggregate.----Liverpool won 1–0 on aggregate.
See main article: 2001 UEFA Cup final.
The final was played on 16 May 2001 at the Westfalenstadion in Dortmund, Germany.