Well that goes without saying. You need the Black Masks to counter Darkja's damage (though there is no protection from its instant death effect) but it will make things less annoying. Scathe is also a must cause Flare takes too long to recover and if memory serves me correct, he has an ability that makes him immune to Holy.

If your levels are high enough, you can beat him easily by knocking him down to a third of his health and then try using a Quickening chain to finish him off in one fell swoop but I never have much luck with Quickenings so I stick to twiddling him down with magic. I ended up manually moving all three party members around him to form a triangle and had each of them spam Scathe. The triangle formation prevents Zodiark from hitting all of your party with Darkja and Scathe.

I'm sure someone has a much better strategy but that's what worked for me and my levels were around 50'ish.