"Waving in dismissal" means that she waved goodbye or that she gestured to be dismissed?

You may say "I signaled her," but "wave" doesn't similarly take a direct object as the target of the gesture. You have to say

I waved at her in dismissal and left the room, only to perceive the fact that she’s never left my mind.

This means that I dismissed her (i.e., told her to leave) with a wave of my hand. (We use the word "dismissive" for the gesture to indicate that the person should leave our presence as no longer worth consideration.) Then I, myself then left the room, only to find that while I could order her to leave my presence, I couldn't get her out of my mind.

(An aside: the tenses don't really work. "Only to perceive" means that the perception follows closely on the dismissal and the leaving, making the present perfect, "she's left" = "she has left", inapt. Better -- "since then I have realized that she never left my mind.")