I would divide the problem in two, formating and comparing. If you can assume that the format is correct, then comparing only numbers version is very simple:
final int versionA = Integer.parseInt( "01.02.00".replaceAll( "\\.", "" ) );
final int versionB = Integer.parseInt( "01.12.00".replaceAll( "\\.", "" ) );
Then both versions can be compared as integers. So the "big problem" is the format, but that can have many rules. In my case i just complete a minimum of two pair of digits, so the format is "99.99.99" always, and then i do the above conversion; so in my case the program logic is in the formatting, and not in the version comparison. Now, if you are doing something very specific and maybe you can trust the origin of the version string, maybe you just can check the length of the version string and then just do the int conversion... but i think it's a best practice to make sure the format is as expected.
