In your question, you left out a previous sentence that is important for figuring out what this means:
This man was called "Beauty" by the other men of the fort.
What your sentence means is that it's an "ironic nickname", like when a two meter tall man is called "Shorty"; see TVtropes.
Antithesis: a person or thing that is the direct opposite of someone or something else.
So Jack London is saying that he was given his nickname because it's the direct opposite of one of his attributes.
EDIT: the OP asked about the grammaticality of the sentence. Here is my answer:
The sentence is inverted (which is grammatical, but somewhat uncommon); in the more usual word order, it says "His naming was due to antithesis." Here, "was due to" means "was because of", and "naming" means being given a name, so put in more everyday language, the sentence becomes "he was given his name because of antithesis."