Will you acquire an accent? Possibly, but you would lose it again as fast as you'd acquired it.
The thing is: there is no dialect-free region in Germany, i.e. wherever you go, you'll be confronted by the local dialect to some extent. However, educated people usually speak with only a very slight regional accent (or none). Therefore, you will be able to understand people at the university of Vienna just fine.
There are a few - but not very many! - words used in Austria which people in Hamburg would not understand, e.g. "Obers" instead of "Sahne" for "cream". But "Grüß Gott" is used as a greeting all over the south of Germany as well.
If I were you, I wouldn't worry too much about this. :)