Boot a Linux emergency disc in EFI mode (the Ubuntu installer in its "try before installing" mode should work). You can then use the efibootmgr utility to delete the unwanted entry. You'll use -v to view the list of options and then a combination of -b and -B to eliminate the ones you don't want:
$ sudo efibootmgr -v
BootCurrent: 0000
Timeout: 0 seconds
BootOrder: 0000,0001,0003
Boot0000* rEFInd Boot Manager HD(1,28,96000,bc34b60c-6611-492f-99b0-d2c37bd77f48)File(\EFI\refind\shim.efi)
Boot0001* fedora HD(1,28,96000,bc34b60c-6611-492f-99b0-d2c37bd77f48)File(\EFI\fedora\grubx64.efi)
Boot0003* ubuntu HD(1,28,96000,bc34b60c-6611-492f-99b0-d2c37bd77f48)File(EFI\Ubuntu\grubx64.efi)
$ sudo efibootmgr -b 3 -B
Some EFIs provide the ability to do this in their own user interfaces, too, but details vary greatly from one to another.