Linus G Thiel says that you cannot do this in javascript. Oddly enough, his answer lists an excerpt from MDN that sounds like it tells how to do this. The line was:
"Providing an empty string for strUrl is a way to get a reference to
an open window by its name without changing the window's location."
I tried this and it works for me.
winref = window.open('', 'thatname', '', true);
winref.close();
However, this may only work if you opened the window from your page. And if that's true, then it's kind of pointless to do a window.open just to get the reference. You probably already have the reference, in that case.