Template:1999 Copa Departamental knockout stage bracket

Round of 16

Quarterfinals

Semifinals

Final

16 September – San Salvador

San Pedro

22 September – San Salvador

Third place (4th)

Winner Match 61

16 September – Adolfosburg

Winner Match 62

Winner Group B

26 September – San Romero (COR)

Third place (3rd)

Winner Match 69

17 September – San Romero (COR)

Winner Match 70

La'Unión

22 September – Adolfosburg (RA1)

Third place (2nd)

Winner Match 63

17 September – Salvador (ESA)

Winner Match 64

San Carlos Islands

30 September – San Salvador

Third place (1st)

Winner Match 73

18 September – San Salvador

Winner Match 74

Winner Group E

23 September – San Romero (COR)

Group runner-up (6th)

Winner Match 65

18 September – Adolfosburg (RA1)

Winner Match 66

Winner Group F

27 September – Salvador (ESA)

Group runner-up (5th)

Winner Match 71

19 September– San Romero (COR)

Winner Match 72

Third-place match

Group runner-up (1st)

23 September – Salvador (ESA)

29 September – Adolfosburg (RA1)

Group runner-up (4th)

Winner Match 67

Loser Match 73

19 September – Salvador (ESA)

Winner Match 68

Loser Match 74

Group runner-up (2nd)

Group runner-up (3rd)