Template:1999 Copa Departamental knockout stage bracket

Round of 16

Quarterfinals

Semifinals

Final

16 September – San Salvador

Winner Group A

22 September – San Salvador

Third place (4th)

16 September – Adolfosburg

Winner Group B

26 September – San Romero

Third place (3rd)

17 September – San Romero

Winner Group C

22 September – Adolfosburg

Third place (2nd)

17 September – Salvador

Winner Group D

30 September – San Salvador

Third place (1st)

18 September – San Salvador

Winner Group E

23 September – San Romero

Group runner-up (6th)

18 September – Adolfosburg

Winner Group F

27 September – Salvador

Group runner-up (5th)

19 September– San Romero

Third-place match

Group runner-up (1st)

23 September – Salvador

29 September – Adolfosburg

Group runner-up (4th)

19 September – Salvador

Group runner-up (2nd)

Group runner-up (3rd)