@tanguatlay,
I believe you meant to write:
All the girls are not intelligent.
Every girl is not intelligent.
Yes, the sentences have the same meaning. As for whether or not they are natural, i would say that a native speaker would write:
Not all the girls are intelligent.
Not every girl is intelligent.
Nevertheless, there is nothing "unnatural" about the sentences. I just think they'd look a little odd, somewhat awkward, to a native speaker.