What options do I have when a journal refuses my paper based on 1/3 review by a non-relevant referee?

Half-joking, half-serious:

Next time you're having some beers with some trusted colleagues, tell this story and gripe about this particular journal. For one, it will blow off some steam. (Caveat: I wouldn't recommend complaining to people you don't know well, at least if you are junior.)

Moreover, in the long run, this is how reputations are built or lost. If your colleagues are as upset by your story as you are, then they might tell it to others, avoid publishing in this journal, and/or decline referee requests from this journal's editors. (Conversely, if your colleagues think you're being unreasonable, you might get some useful advice.)

This would have only a minor effect of course, but it would do more than contacting the publisher: in the long run, authors hold all the cards, as a journal is only as good as the papers that get submitted to it.

When submitting papers you will often get reviewers who dislike your work for various reasons. Often their reviews will leave you scratching your head wondering how they misunderstand your work so badly. This is normal. You got it particularly bad with this happening after a major revision.

If you have the option of a rebuttal, you should politely mention why you disagree with the reviewers' points and hope for the best. Failing that, there's nothing you can really do. Your best option is to throw your hands in the air, curse loudly, and then resubmit elsewhere.

If you want this not to go unnoticed, you can apply Anonymous' suggestion and also write a polite but clear e-mail to the editor and the editor in chief of the journal explaining why you consider the handling of your paper unsatisfactory. This may carry more weight if you make it clear that you do not try to change the decision and are already submitting elsewhere.

I would only recommend this if you are in a position where the handling editor cannot hurt your career too badly (e.g. tenured, or working mainly in a different field), as he or she may keep a grudge.

A very minor action you can also take without any risk is to write your very first name on your black list of editors you will never again submit to, and will never referee for.