There is not a canonical "D&D" answer. The answer differs per campaign world.
I know it's a little weird - the D&D 3 core books don't present themselves as a generic system per se; they hint at a shared cosmology with the gods, certain roles for the races, etc. that makes it seem like there's a larger world there. But it's just a hollow shell, to be filled in either by yourself or by the specific campaign worlds (Forgotten Realms, Greyhawk, Golarion, etc.).
Now, in 3e/3.5e Greyhawk is the default setting (they didn't follow through on that real well but it was stated) so you could look to the Greyhawk answers as the canonical defaults. I don't know that they ever answered the "but where did they all come from" questions, and I was a Greyhawk aficionado for decades. Canonfire! would be the place to research that. If you're looking for Corellon specifically, try this wiki article. Most campaign worlds are deliberately cagy about how exactly the beginning of all things transpired, however, and Greyhawk is especially so.
According to Netheril: Empire of Magic (N:EoM), at the time of the Netherese there were very few human deities and each one of them carried very many portfolios. It seems like as the millennia went by, those portfolios got shared by many new powers.
For Mystryl, the list went like this: Magic, spells, the weave, wizards, spellcasters, energy, creativity, knowledge, invention, song, time, spring (page 49 of The Winds of Netheril).
We can compare this list with the portfolios given in the FR Adventures (FRA) and Faiths & Avatars (F&A) sourcebooks. We see that every portfolio except Time is covered: Azuth (mages, energy according to FRA; wizards, spellcasters according to F&A), Oghma (knowledge according to FRA; knowledge, invention according to F&A), Lathander (spring according to FRA; spring, creativity according to F&A), Milil (song), and of course Mystra (magic, spells, the weave).
Given that every other one is somehow covered, and the great many commonalities between N:EoM and F&A, I would agree with Carcer's statement and say Time appears to have been intentionally left out by TSR. (F&A lists Julia Martin with Eric Boyd as designers. For N:EoM, Julia Martin is listed under "additional design" and Eric Boyd is listed as a proofreader.)
There is one final curiosity: Amaunator is mentioned (in both N:EoM and F&A) to have misinterpreted some godly contract and wanted to preside over passage of time, but decided not to interfere with Mystryl. It looks like after Mystryl's demise, he still did not claim Time. So perhaps Mystra could still be the "hidden inheritor" of the portfolio and might someday claim it openly. It might also be worth mentioning that three "time gates" that allow characters to travel back to the Netherese period were still active as of 1370DR, and they were being protected by Mystryl's magic (N:EoM). It would be an interesting scenario to have Midnight/Mystra sending an avatar/proxy to meet her old self, Mystryl.
On a related note: Here is a list of powers from F&A who grant major access to the sphere of Time to her/his speciality priests: Amaunator, Auril, Chauntea, Cyric, Eldath, Kelemvor, Leira, Mask, Mielikki, Myrkul, Mystra, Shar, Silvanus, Sune. We broadly see that they are mostly deities of nature, death, or deception. If you really want to assign the portfolio of Time in your own game, consider one of these.
Deities followed by chronomancers
There is an article with the title Chronomancy & the Multiverse, version 1.1 by Roger E. Moore, published as "an updated and expanded excerpt from the Chronomancer", a 2e accessory. The article was made public by the WotC on their free downloads for previous editions site. This article has a section of the effects of chronomancy in the Realms, and relates time with deities of knowledge and writing. It is stated:
Native chronomancers are usually devout followers of both a deity of magic (e.g., Mystra) and a deity of time or history (e.g., Deneir or Oghma), serving as historians and information collectors. Elven chronomancers of Labelas Enoreth are possible. Shou Lung, in Kara-Tur, might have a secret, officially approved group of chronomancers, probably Historians, working for the Emperor.
Best Answer
Ao created tablets of new rules intended to restore peace and balance to Toril.
In a video of a 2012 Gencon panel featuring Forgotten Realms novel authors, What is the Sundering (Part 1), it is stated that the supreme overgod Ao intentionally re-created the tablet of rules that separated the worlds of Abeir and Toril, intended to restore balance and order to Toril.
The events of the D&D 4th edition era where the now twin worlds of Abeir and Toril were recombined into one world are revealed to be the result of Ao destroying tablets of rules he created, those that divided the worlds in the first place long ago. Originally, their purpose was to divide the world into Abeir, where the Primoridials held sway, and Toril, where the Gods had power.
However, when two deities stole the tablets and began fighting amongst each other, Ao destroyed them to teach the gods a lesson, and the worlds were recombined. Unfortunately, this only made things worse, and so Ao set about recreating the tablets and dividing Abeir and Toril in two once more, but this time with a new rule limiting the ability of the gods to damage Toril in their petty squabbles.
Ao's reasons are described at 11:35 in the video:
This ethos reflects Wizards of the Coast's policy for the focus of Realms products and novels, which we learn at 23:20 in the video is intended to return to "the heart of high fantasy", and at 31:15 it is stated that WotC wants individual characters to be significant actors (e.g. why player characters should have to save the day instead of leaving it to deities).
As such the novels of that era will focus on the actions of people, not the gods or Ao. It may be that no novel or sourcebook explicitly references this lore about Ao stated by Wizards of the Coast. At 36:48 in the video, it is said to be likely that no protagonist of these novels is likely to be fully aware of the situation with the gods, and even Elminster may only partially understand it.
It should be noted that gods can, to some extent, defy Ao. It was gods who stole the tablets from Ao in the first place, and Tiamat has a loophole which allows her to be summoned in person to Toril. This suggests that Ao's new rules are significant, but not necessarily absolute.