This is from Pride and Prejudice. The man (Mr. Darcy) is the type of guy who judges women immediately by how pretty they are, and how well placed they are in society. He wants to dismiss Elizabeth, but there is something about her that he finds attractive. This passage is about that moment. I will rephrase it...
He said to himself AND HIS FRIENDS that her face was not attractive. But as soon as he said those words he began to see how her face was intelligent, and that she had a beautiful expression in her dark eyes. Once he discovered this fact he soon discovered some others which were equally surprising. He still noticed that her face was not perfectly symmetrical, but he was forced to acknowledge her figure to be light and pleasing. He also realized, all of a sudden, that he was wrong to say that her manners were not fashionable. In fact, now that he looked at her again, he was caught by their playfulness and friendly manner.
So what he is saying here is....I looked at her and quickly decided that she was not attractive and beneath my level in society, but when I looked at her a second time I was surprised to see how wrong I was.
(rendered uncommonly intelligent) - old fashioned way of saying her face appeared, suddenly, to be intelligent. In other words, RENDERED = he just noticed it.
(others equally mortifying) - He found her attractive and this shocked him (mortified him). Then he began to notice other things and they shocked him just as much. They were EQUALLY mortifying.
(failure of perfect symmetry) - Really beautiful people are often very symmetrical (both sides of their face are perfectly the same). He still sees that she is NOT perfectly symmetrical. Perhaps one eye is bigger than the other, or maybe her mouth is a little crooked, but even so he finds her attractive. And he is SURPRISED that he finds her attractive.