You can try EQ'ing it out slightly.
But if it's really important to get rid of it on a background track, you can record each chord on separate tracks.
ie, play all the A chords on track 1 (stop playing and leave silence when other chords should be playing.)
Go back and record all the B chords on track 2 (leaving silence where track 1 is)
Keep going until you've got the whole song covered and then combine everything onto one track. If you do it right, it'll sound like one player