As long as the ISO of the backup was patched to match the region code of your Saturn before it was burned to CD-R, you should be able to play it using the swap trick. For example, if you have a U.S./Canada Saturn, then you'll need to patch the region code of the ISO of your Japanese game to 'U' "For USA and CANADA." before you burn it to CD-R. Likewise, if you have an European Saturn, you'll need to patch the region code of the ISO of your Japanese game to 'E' "For EUROPE." before burning. If you have already burned the Japanese game to CD-R without patching the region code and you don't feel like re-burning, you can use one of the territory converter cartridges (e.g., Action Replay 4M Plus, ST Key) combined with the swap trick to play the backup, but keep in mind that performing the swap trick with a cartridge is a bit different than the normal way of swapping.
Patching the ISO before burning or use a territory converter cartridge to bypass the territory protection.