The talmud at the very end of Chullin 26b says that on Motzaei Yom Tov we still say the phrase "bein yom ha'shevii l'sheshet y'mei hama'aseh" in havdallah, even though this phrase is irrelevant to Yom Tov.
The question is, why did Chazal not establish a more targeted nusach for Yom Tov havdallah that would be more appropriate, e.g. "bein kedushat Yom Tov l'sheshet y'mei hama'aseh"?
The idea of this Berachah is to praise Hash-m for creating different things in the world and not making everything the same. Just as everyone understands that there is a tremendous difference between light and dark, we praise Hash-m for giving us the great gift of Shabbos, which is totally different from the other days of the week, and in a similar way we thank Hash-m for making the other distinctions in the world that we mention in Havdalah.
Accordingly, it is not necessary to mention the specific level of Kedushah involved with this particular Yom Tov, because we are expressing our gratitude for the general distinction between the holy and the profane which all comes from Hash-m.