  I believe you can accomplish this by entering the BIOS, and under integrated devices click on slot disablement. For the specific PCIe slot set the slot disablement to "Boot Driver Disabled". This will allow the slot to be visible to the OS, but will not be available as a boot device.
How we can disable LSI SAS HBA from boot ? I have JBOD connected to it and not want to scan and attempt to boot during reboot or boot process
R720 disabled LSI SAS HBA from Boot