One solution would be to auto-fill the inputs with whitespace characters, and have them clear on focus.
Example: http://nfdb.net/autofill.php
<!doctype html>
<html>
<head>
<title>Autofill Test</title>
<script>
var userfield;
// After the document has loaded, manipulate DOM elements.
window.addEventListener('load', function() {
// Get the username field element.
userfield = document.getElementById('user');
// Listen to the 'focus' event on the input element.
userfield.addEventListener('focus', function() {
// Checks if the value is the EM space character,
// and removes it when the input is recieves focus.
if (this.value == '\u2003') this.value = ''
}, false);
// Listen to the 'blur' event on the input element.
// Triggered when the user focuses on another element or window.
userfield.addEventListener('blur', function() {
// Checks if the value is empty (the user hasn't typed)
// and inserts the EM space character if necessary.
if (this.value == '') this.value = '\u2003';
}, false);
}, false);
</script>
</head>
<body>
<form method="GET" action="">
<input id="user" name="username" type="text" value=" "/><br/>
<input name="password" type="password" value=""/><br/>
<input type="submit" value="Login">
</form>
</body>
</html>
This should stop the browser from auto-filling the fields, but still allow them to auto-complete.
Here's another example that clears the form inputs after the page loads. The advantage of this method is that the inputs never have any whitespace characters in them, the disadvantage is that there's a small possibility that the auto-filled values may be visible for a few milliseconds.
<!doctype html>
<html>
<head>
<title>Autofill Test</title>
<script>
var userfield, passfield;
// Wait for the document to load, then call the clear function.
window.addEventListener('load', function() {
// Get the fields we want to clear.
userfield = document.getElementById('user');
passfield = document.getElementById('pass');
// Clear the fields.
userfield.value = '';
passfield.value = '';
// Clear the fields again after a very short period of time, in case the auto-complete is delayed.
setTimeout(function() { userfield.value = ''; passfield.value = ''; }, 50);
setTimeout(function() { userfield.value = ''; passfield.value = ''; }, 100);
}, false);
</script>
</head>
<body>
<div>This form has autofill disabled:</div>
<form name="login" method="GET" action="./autofill2.php">
<input id="user" name="username" type="text" value=""/><br/>
<input id="pass" name="password" type="password" value=""/><br/>
<input type="submit" value="Login">
</form>
<div>This form is untouched:</div>
<form name="login" method="GET" action="./autofill2.php">
<input name="username" type="text" value=""/><br/>
<input name="password" type="password" value=""/><br/>
<input type="submit" value="Login">
</form>
</body>
</html>