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| 1st(1st leg) | Vitória Setúbal | - | ACF Fiorentina | 3:0 (2:0) | ||
| 2nd (2nd leg) | ACF Fiorentina | - | Vitória Setúbal | 2:1 (2:0) | ||
| 1st(1st leg): 18/12/1968 | 2nd (2nd leg): 22/01/1969 | Winner: Vitória Setúbal | ||||
| 1st(1st leg) | Hamburger SV | - | Hibernian FC | 1:0 (1:0) | ||
| 2nd (2nd leg) | Hibernian FC | - | Hamburger SV | 2:1 (0:0) | ||
| 1st(1st leg): 18/12/1968 | 2nd (2nd leg): 15/01/1969 | Winner: Hamburger SV | ||||
| 1st(1st leg) | Leeds United | - | Hannover 96 | 5:1 (2:0) | ||
| 2nd (2nd leg) | Hannover 96 | - | Leeds United | 1:2 (0:2) | ||
| 1st(1st leg): 18/12/1968 | 2nd (2nd leg): 04/02/1969 | Winner: Leeds United | ||||
| 1st(1st leg) | Real Zaragoza | - | Newcastle United | 3:2 (2:2) | ||
| 2nd (2nd leg) | Newcastle United | - | Real Zaragoza | 2:1 (2:1) | ||
| 1st(1st leg): 01/01/1969 | 2nd (2nd leg): 15/01/1969 | Winner: Newcastle United | ||||
| 1st(1st leg) | Athletic Bilbao | - | Eintracht Frankfurt | 1:0 (1:0) | ||
| 2nd (2nd leg) | Eintracht Frankfurt | - | Athletic Bilbao | 1:1 (1:1) | ||
| 1st(1st leg): 08/01/1969 | 2nd (2nd leg): 29/01/1969 | Winner: Athletic Bilbao | ||||
| 1st(1st leg) | DWS Amsterdam | - | Rangers FC | 0:2 (0:1) | ||
| 2nd (2nd leg) | Rangers FC | - | DWS Amsterdam | 2:1 (2:1) | ||
| 1st(1st leg): 15/01/1969 | 2nd (2nd leg): 22/01/1969 | Winner: Rangers FC | ||||
| 1st(1st leg) | OFK Beograd | - | Göztepe | 3:1 (1:0) | ||
| 2nd (2nd leg) | Göztepe | - | OFK Beograd | 2:0 (2:0) | ||
| 1st(1st leg): 22/01/1969 | 2nd (2nd leg): 29/01/1969 | Winner: Göztepe | ||||
| 1st(1st leg) | Legia Warszawa | - | Újpesti Dózsa SC | 0:1 (0:0) | ||
| 2nd (2nd leg) | Újpesti Dózsa SC | - | Legia Warszawa | 2:2 (0:2) | ||
| 1st(1st leg): 23/02/1969 | 2nd (2nd leg): 26/02/1969 | Winner: Újpesti Dózsa SC | ||||
