Before it had displayed any power, Indy tells Marian to close her eyes, and keep them closed, no matter what happens. Kat was perplexed as to why Indy was putting any stock into the legends of the Ark, and more importantly, how he knew that not looking would save them.

Because. Herein lies the distinction between fact (or knowledge) and truth (belief). Indiana knew the myths, that one can not look upon the face of the Hebrew god and live, and so, when things got weird, he acted on the knowledge, at a point when it seemed maybe there was something to the stories after all and he had little to lose in an act of faith.