Just copy their autoloader functions to a separate file, rename them, and hook them up with spl_autoload_register
thus:
<?php
function loadFrameworkOne($name) {
// contents of __autoload from framework one.
}
function loadFrameworkTwo($name) {
// contents of __autoload from framework two.
}
spl_autoload_register('loadFrameworkOne');
spl_autoload_register('loadFrameworkTwo');
This is quick, dirty and off the top of my head ;)