"Você" refers to the 2nd person (Tu) using the 3rd conjugation (Ele/Ela).
It's the way we speak in Brazil. And this is a good thing, because this way you have to remember less conjugations.
First thing: Don't try literal translations in any language, I recommend you to understand the idea behind the expresions, ok? It's because, very often, you will see that one word can mean different things in other cultural context. :)
Here, we have a lot of words to express "YOU" in Portuguese. It sounds complexe, but it's easy when you know the rules and the structure.
In portuguese, we have some types of PRONOUNS. I'm going to explain two of them.
1. Pronomes pessoais do caso reto [Subject pronoun].
2. Pronomes de tratamento [Pronouns refers to the 2nd subject pronoun - YOU - but with the 3rd conjugation. Theoretically this serves to indicate degree of formality, like "Sr" or "Mr" in English, or "Usted" in Spanish. BUT in Brazil we use one of those "Treatment Pronouns" - VOCÊ - instead of "tu"].
Tu és = You are
Você é = You are
Ele/Ela é = He/She/It is