NOTE : System Navigation will still appear when ever you show any AlertDialog but when you dismiss it , It will hide again. If you still not want this behavior then use Center View to create Alert like view.
You can try following approach which i have used . 
/**
     * Hide system NavigationBar and StatusBar
     */
    @TargetApi(Build.VERSION_CODES.KITKAT)
    public void hideNavigationBar()
    {
        final View decorView = getWindow().getDecorView();
        decorView.setOnSystemUiVisibilityChangeListener (new View.OnSystemUiVisibilityChangeListener() {
            @Override
            public void onSystemUiVisibilityChange(int visibility) {
                Log.i("LOG","Menu Shown is this"+ visibility);
                decorView.setSystemUiVisibility(View.SYSTEM_UI_FLAG_LAYOUT_STABLE
                        | View.SYSTEM_UI_FLAG_LAYOUT_HIDE_NAVIGATION
                        | View.SYSTEM_UI_FLAG_HIDE_NAVIGATION
                        | View.SYSTEM_UI_FLAG_IMMERSIVE);
            }
        });
    }
Call above method from onResume of Activity and make sure you override following method in activity.
@Override
    @TargetApi(Build.VERSION_CODES.KITKAT)
    public void onWindowFocusChanged(boolean hasFocus) {
        super.onWindowFocusChanged(hasFocus);
        if (hasFocus)
        {
            getWindow().getDecorView().setSystemUiVisibility(
                    View.SYSTEM_UI_FLAG_LAYOUT_STABLE
                            | View.SYSTEM_UI_FLAG_LAYOUT_HIDE_NAVIGATION
                            | View.SYSTEM_UI_FLAG_HIDE_NAVIGATION
                            | View.SYSTEM_UI_FLAG_IMMERSIVE
                            );
        }
    }
You should use following approach to hide navigation when Alert created.
public static void showAlert(Context context,String title,String message) {
        AlertDialog.Builder alertDialogBuilder = new AlertDialog.Builder(context);
        alertDialogBuilder.setTitle(title);
        alertDialogBuilder.setMessage(message);
        alertDialogBuilder.setCancelable(false);
        alertDialogBuilder.setPositiveButton("OK", new DialogInterface.OnClickListener() {
            public void onClick(DialogInterface dialog, int id) {
                dialog.cancel();
            }
        });
       final AlertDialog alertDialog = alertDialogBuilder.create();
        //Here's the magic..
//Set the dialog to not focusable (makes navigation ignore us adding the window)
        alertDialog.getWindow().setFlags(WindowManager.LayoutParams.FLAG_NOT_FOCUSABLE, WindowManager.LayoutParams.FLAG_NOT_FOCUSABLE);
        alertDialog.show();
        //Set the dialog to immersive
        alertDialog.getWindow().getDecorView().setSystemUiVisibility(
                ((Activity)context).getWindow().getDecorView().getSystemUiVisibility());
//Clear the not focusable flag from the window
       alertDialog.getWindow().clearFlags(WindowManager.LayoutParams.FLAG_NOT_FOCUSABLE);
    }
I found above working code from this SO