I have a form with id theForm which has the following div with a submit button inside:
You can use...
document.getElementById('theForm').submit();
...but don't replace the innerHTML. You could hide the form and then insert a processing... span which will appear in its place.
var form = document.getElementById('theForm');
form.style.display = 'none';
var processing = document.createElement('span');
processing.appendChild(document.createTextNode('processing ...'));
form.parentNode.insertBefore(processing, form);