It sounds strange because the way it is worded means that the teacher is closing the boy's eyes. Normally we only close our own eyes. It might be more common to "cover" someone's eyes (meaning to place your hand over their eyes, so they can't see even if their eyes are still open)

I agree with Jennifer. Parents often cover a child's eyes. You only close another person's eyes if they are dead. It means you move the eyelids with your fingers to a closed position.

"as she closed his eyes" is more concise, but otherwise it reads fine. It is describing what sounds like quite a surreal event, though: my teachers never closed my eyes.