Javascript and PHP do not directly interact (exceptions apply, don't worry about them now :D). The best way to implement this type of interaction between these two disparate languages is to use the query string or cookies.
I think there may be some confusion here about when and how PHP is executed as opposed to when and how javascript is executed. Think of PHP as the factory - the goods are physically produced there. Think of your server as the loading dock, the internet as the shipping company. Your browser is the store, HTML is the shelves; Javascript is the window decorations on the store that sells the merchandise. The window decorations have no affect on the production, the factory can make some window decorations, but it doesn't use them, it just ships them right along with the merchandise for the store to use. PHP is the factory, javascript is the decoration. There are some problems with taking this analogy too literally, but there it is in a nutshell.
You can make the PHP redirect conditional on the presence or absence of a specific query string variable:
<?php
// redirect if $_GET['no_redirect'] is NOT set. Reverse the true/false to invert this rule
$do_redirect = (isset($_GET['no_redirect']) === false ? true : false);
// perform the redirect, if required
if ($do_redirect === false)
header('Location:http://mydomain.com');
?>
Javascript:
window.location = 'http://mydomain.com/?no_redirect=1';
EDIT If you're trying to detect if javascript is enabled, then the best way is for javascript to set a cookie if it is enabled. PHP can then check for this cookie, and if it isn't found then you'll know that javascript didn't get a chance to set it, so it must be disabled (or the user edited their cookies).
Take a look at some code snippets for dealing with cookies in javascript, and check out the documentation for dealing with cookies in PHP.
header("Location: URL"). With this, the redirect happens before the page is loaded - thus JavaScript has no chance to load, let alone execute.