In my opinion, Ganon had it ever since Zelda sent Link back. Since Link would have still had the Triforce of Courage, this would cause the rest of the Triforce to be sent to their respective owners. Ganon just did not realize this for a while (Just because you have the Triforce doesn't mean you know you do, Link did not realize he had it until he was told so in OoT) So when Ganon realized he had it some time later, he went on his rampage and that is when the Sages sealed him in the Twilight Realm.

And Link had to have had the ToC in TP because otherwise he wouldn't turn into a wolf in the Twilight Realm (remember, it was shiny when he first transformed)

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I am no longer leader of the Humulation Army, as I am gone. For admittance into the Army, please check PM Hombre de Mundo, the new leader.
-humulos.com---"I'm a Thwomp. I thwomp people."---ZU: The Nicest Place on Earth -
I have gone on my Mission! I won't be able to chat here for 2 years, so don't PM me! It will just be wasted bandwith... Look forward to seeing you all when I get back!