The pattern passed to String.split has the regular expression syntax, thus the java.util.regex package is the place to look for additional tools for dealing with them, like quoting a string to enforce literal matching.
So a solution only using system properties and string operations would look like
String path=System.getProperty("your.property"), sep=System.getProperty("file.separator");
for(String s: path.split(Pattern.quote(sep)))
System.out.println(s);
However, there is no reason not to use the dedicated APIs:
Path path = Paths.get(System.getProperty("your.property"));
if(path.isAbsolute()) System.out.println(path.getRoot());
for(Path p: path)
System.out.println(p);
Note that this also handles root paths correctly, i.e. on Windows, the root of a drive is like C:\, not C:, and on Linux, the root is /, not an empty string, and both cases are not handled correctly when just splitting at the separator chars.
Even before Java 7, there was an API that could handle this:
File path = new File(System.getProperty("your.property"));
for(File f = path; f != null; f = f.getParentFile())
System.out.println(f.getName().isEmpty()? f.getPath(): f.getName());
though the code will iterate the elements in the opposite order.
Note, how simple your specific task of splitting at two levels above the path becomes with the dedicated API:
Path path = Paths.get(System.getProperty("your.property"));
Path first = path.getParent().getParent(), second = first.relativize(path);
System.out.println("first: "+first);
System.out.println("second: "+second);