| 9 | Roy Makaay | First Group Stage | UEFA Champions League 02/03 |
| 6 | Walter Pandiani | Group Stage | UEFA Champions League 03/04 |
| 6 | Diego Tristan | First Group Stage | UEFA Champions League 01/02 |
| 5 | Walter Pandiani | First Group Stage | UEFA Champions League 00/01 |
| 4 | Albert Luque | Group Stage | UEFA Champions League 03/04 |
| 4 | Diego Tristan | First Group Stage | UEFA Champions League 02/03 |
| 3 | Diego Tristan | Group Stage | UEFA Champions League 03/04 |
| 3 | Juan Carlos Valeron | First Group Stage | UEFA Champions League 01/02 |
| 3 | Djalminha | Second Group Stage | UEFA Champions League 00/01 |
| 2 | Juan Carlos Valeron | Group Stage | UEFA Champions League 03/04 |
| 2 | Victor | First Group Stage | UEFA Champions League 02/03 |
| 2 | Djalminha | Second Group Stage | UEFA Champions League 01/02 |
| 2 | Noureddine Naybet | First Group Stage | UEFA Champions League 01/02 |
| 2 | Noureddine Naybet | First Group Stage | UEFA Champions League 00/01 |
| 2 | Roy Makaay | First Group Stage | UEFA Champions League 00/01 |
| 2 | Victor | First Group Stage | UEFA Champions League 00/01 |
| 2 | Diego Tristan | Second Group Stage | UEFA Champions League 00/01 |
| 1 | Hector | Group Stage | UEFA Champions League 03/04 |
| 1 | Lionel Scaloni | Group Stage | UEFA Champions League 03/04 |
| 1 | Fran | Quarter-finals | UEFA Champions League 03/04 |
| 1 | Sergio | Group Stage | UEFA Champions League 03/04 |
| 1 | Joan Capdevila | First Group Stage | UEFA Champions League 02/03 |
| 1 | Cesar | First Group Stage | UEFA Champions League 02/03 |
| 1 | Fran | First Group Stage | UEFA Champions League 01/02 |
| 1 | Sergio | First Group Stage | UEFA Champions League 01/02 |
| 1 | Walter Pandiani | First Group Stage | UEFA Champions League 01/02 |
| 1 | Joan Capdevila | First Group Stage | UEFA Champions League 01/02 |
| 1 | Roy Makaay | Second Group Stage | UEFA Champions League 01/02 |
| 1 | Turu Flores | Second Group Stage | UEFA Champions League 00/01 |
| 1 | Lionel Scaloni | First Group Stage | UEFA Champions League 00/01 |
