I think the Arcane Age and Karsus's Fall entered canon sometime around 1995-1996.
Karsus was described as a "lesser-known" deity in a half-page article by Eric Boyd published in the February 1995 issue (#104) of the PolyhedronPolyhedron magazine. At this point, Karsus'sKarsus is not a dead power and his demise (from greater deity to demigod) was attributed to his poisoning by a Netherese mage named Wulgreth, who sought to steal immortality from Karsus (ironic, isn't it?). So we can conclude that early 1995, Karsus's story as we know it was not yet canon.
TSR released the Netheril: Empire of Magic (N:EoM) boxed set in November 1996. Yet we can argue that Netheril storyline was already entering the FR canon before N:EoM's publication based on evidence from the sourcebook Faiths and Avatars (F&A), which was published in March of that year. F&A has plenty of information about Mystra that foretells the then-upcoming Arcane Age storyline: Mystryl is given as one of Mystra's aliases; her speciality priests can also be of the CN alignment (Mystrl was CN); one of Mystra's symbols is none other than Mystrl's symbol, a single blue-white star. It is worth noting that one of the authors of F&A was Eric Boyd.
Powers and Pantheons (P&P), a companion to and continuation of F&A, was published in 1997. At this point it is clear that the whole Karsus story is canon: P&P lists Karsus as a dead demigod, describing explicitly the events in the earlier Netheril material; including his 12th level spell, and how he used it to steal Mystrl's power and ended up dead.
1998 saw the expansion of the Arcane Age material further with the publication of Cormanthyr: Empire of Elves. This product is also in full support of the Karsus's Fall story, including all the events in the earlier Arcane Age material.
The conclusion is that Karsus's Fall became canon during the 2e of AD&D.