The exclamation mark should go at the end of the sentence where you express your realization of the situation. Here's how you can incorporate it:
"I was frozen in shock. I didn't cry, nor break down; I just stood there, waiting for her to stop whimpering and to stand up and to go back to how it was 10 minutes before, her running around the courtyard, but she didn't. She stopped whimpering eventually, but her eyes started to close, and that's when I realized the situation!"
The exclamation mark emphasizes the impact of your realization.