Yes, it is definitely different, even to the extent of being a different dialect with some different vocabulary as well as different pronunciation. But then, so is the Low German that is spoken in some places in northern Germany. Berlin (towards the north) has its own distinct pronunciations too, as do many other locations.
A couple of examples of southern German (Bavarian):
(1) The word for "two" in standard German is "zwei" and in Bavarian it is "zwo."
(2) A famous one that Bavarians enjoy teaching newcomers is "squirrel's tail"; in standard Hochdeutsch the word is "Eichhörnchenschwanz"; in Bavarian it is "Oachkatzelschwoaf."
A simplified way to describe the difference between pronunciation in standard German and in southern German would be that in the south, the speaker's mouth and throat are more open in the back (towards the throat) and more relaxed overall; in standard German, the pronunciation tends to occur more towards the front of the mouth and the musculature overall has more tension. This doesn't begin to cover the differences, but is only intended to give an overview.