The solution that works for Sphinx is to prefix the reference with ~.

Per the Sphinx documentation on Cross-referencing Syntax,

If you prefix the content with ~, the link text will only be the last component of the target. For example, :py:meth:`~Queue.Queue.get` will refer to Queue.Queue.get but only display get as the link text.

So the answer is:

class MyClass():
    def foo(self):
        print 'foo'
    def bar(self):
        """This method does the same as :func:`~mymodule.MyClass.foo`"""
        print 'foo'

This results in an HTML looking like this : This method does the same as foo(), and foo() is a link.

However, note that this may not display in Spyder as a link.