What you have done should work, so I suspect something is typed wrong or in the wrong place in your file. Here is a complete working example file:
<!DOCTYPE html>
<html>
<head>
<title>MathJax Macros Configuration</title>
<script type="text/x-mathjax-config">
MathJax.Hub.Config({TeX: {Macros: {phi:"\\varphi"}}});
</script>
<script src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML"></script>
</head>
<body>
phi \(\phi\) and varphi \(\varphi\) should both be the same.
</body>
</html>