Word for "from this point of the document on it will be called simply XYZ"

The usual wording, I believe, is "hereafter/henceforth referred to as".

This document defines the intended behaviour for the AVI to XYZ conversion tool (hereafter referred to as "Conversion Tool").

I've also seen it being dropped completely, as in:

This document defines the intended behaviour for the AVI to XYZ conversion tool ("Conversion Tool").

I've always read your second example clearly without any ambiguity. I prefer that phrasing just because it's uncomplicated. edit: Consider capitalizing the phase whenever it appears as RegDwight did, to make sure it's obvious later in the text

You could try "hereinafter Conversion Tool", although you may find it a little pretentious or legalistic.

Whilst hereinafter may be a bit pretentious, it seems to me more suitable if "referred to as" is to be discarded, as you have. Usually one seeks a shorter 'handle' for subsequent references though. Ideally an acronym. The first time the complete name is given, just put the acronym in brackets immediately after it. No need for any explanatory words at all. Maybe OP really wants to call his app "Conversion Tool", but for the purposes of documentation I'd rather just call it AXCT and be done with it.

I just got a document back from a legal department that replaced every single instance I used "hereafter" with "hereinafter".