After a lot of searching on the internet, I managed to get the System Bar to hide and appear in a 4.2 device using:
To Hide:
Runtime.getRuntime().exec("service call activity 42 s16 com.android.systemui");
Or use 79 instead of 42 for API less than 14. You may also need to include the SET_DEBUG_APP permission, in which case you need to have the application signed with the system key or installed in the /system/app/ directory.
To Show:
Runtime.getRuntime().exec("am startservice --user 0 -n com.android.systemui/.SystemUIService");
If using API 4.0 to 4.1, remove the --user 0 option. Alternatively some people have used the -a (instead of -n) option, though this was causing an error on my device:
Error: Not found; no service started.