You can use {{ variable }} anywhere in your template, not just in the HTML part. So this should work:
<html>
<head>
<script>
var someJavaScriptVar = '{{ geocode[1] }}';
</script>
</head>
<body>
<p>Hello World</p>
<button onclick="alert('Geocode: {{ geocode[0] }} ' + someJavaScriptVar)" />
</body>
</html>
Think of it as a two-stage process: First, Jinja (the template engine Flask uses) generates your text output. This gets sent to the user who executes the JavaScript he sees. If you want your Flask variable to be available in JavaScript as an array, you have to generate an array definition in your output:
<html>
<head>
<script>
var myGeocode = ['{{ geocode[0] }}', '{{ geocode[1] }}'];
</script>
</head>
<body>
<p>Hello World</p>
<button onclick="alert('Geocode: ' + myGeocode[0] + ' ' + myGeocode[1])" />
</body>
</html>
Jinja also offers more advanced constructs from Python, so you can shorten it to:
<html>
<head>
<script>
var myGeocode = [{{ ', '.join(geocode) }}];
</script>
</head>
<body>
<p>Hello World</p>
<button onclick="alert('Geocode: ' + myGeocode[0] + ' ' + myGeocode[1])" />
</body>
</html>
You can also use for loops, if statements and many more, see the Jinja2 documentation for more.
Also, have a look at Ford's answer who points out the tojson filter which is an addition to Jinja2's standard set of filters.
Edit Nov 2018: tojson is now included in Jinja2's standard set of filters.