It was argued that the Welsh National Anthem Hen Wlad Fy Nhadau (Land Of My Fathers) should be played as well as GSTQ, but the FL rejected this decision arguing that GSTQ is the British national anthem so also applies to Wales.
The two sides agreed to drop the GSTQ for all three divisional play-off finals.
FL spokesman John Nagle said: "The national anthem has only ever been sung at play-off weekends because it is regarded as a traditional part of the pre-match build-up to football finals.
"Unfortunately the playing of the anthem this weekend has become a subject of some controversy. This has begun to detract from the games themselves and from the achievements of the clubs involved and this should clearly not be the case.
"The League has always made it clear that it regards these games as domestic club matches. They are neither international matches nor international occasions. Therefore on reflection it is our view that it would be preferable for fans to participate in the singing of their club songs half an hour before kick-off instead of any national anthems."