2008–09 UEFA Champions League Third qualifying round Third qualifying round

| Team_1 | Agg_ | Team_2 | _1st_leg | _2nd_leg |
|---|---|---|---|---|
| Anorthosis | 3–1 | Olympiacos | 3–0 | 0–1 |
| Vitória Guimarães | 1–2 | Basel | 0–0 | 1–2 |
| Shakhtar Donetsk | 5–1 | Dinamo Zagreb | 2–0 | 3–1 |
| Schalke 04 | 1–4 | Atlético Madrid | 1–0 | 0–4 |
| Aalborg BK | 4–0 | Kaunas | 2–0 | 2–0 |
| Barcelona | 4–1 | Wisła Kraków | 4–0 | 0–1 |
| Levski Sofia | 1–2 | BATE Borisov | 0–1 | 1–1 |
| Standard Liège | 0–1 | Liverpool | 0–0 | 0–1 ( aet ) |
| Partizan | 3–4 | Fenerbahçe | 2–2 | 1–2 |
| Twente | 0–6 | Arsenal | 0–2 | 0–4 |
| Spartak Moscow | 2–8 | Dynamo Kyiv | 1–4 | 1–4 |
| Juventus | 5–1 | Artmedia Petržalka | 4–0 | 1–1 |
| Brann | 1–3 | Marseille | 0–1 | 1–2 |
| Fiorentina | 2–0 | Slavia Prague | 2–0 | 0–0 |
| Galatasaray | 2–3 | Steaua Bucureşti | 2–2 | 0–1 |
| Sparta Prague | 1–3 [C ] | Panathinaikos | 1–2 | 0–1 |