As an American (who has lived in the midwest and east coast), a common phrase I would use is
Shield her eyes!
to indicate covering their eyes so they cannot see. This has the same meaning as "cover", but the use of "shield" adds a sense of urgency or need to avoid danger. Because it sounds exaggerated, I most often hear this in playful and joking contexts. (For example, I was very shy and modest when I was younger, and a friend teased me by saying "oh no, shield your eyes!" when two characters had a PG kissing scene in a movie.)
Note that "shield" can also mean "protect" in a purely functional sense, as in the case of debris or wind, which does not necessarily imply that the person is unable to see. The context should make it clear which is meant, but to avoid ambiguity or for a more serious situation,
Cover her eyes!
is appropriate and to-the-point. It would seem a little strange to specify "with your hands", since that is already the most likely method of covering someone's eyes. But if you would like to specify,
Put your hands over her eyes.
is a natural way to phrase it, since the use of "put" requires that you explain what you are going to use, rather than tacking on a prepositional phrase to the "cover" sentence.