You will need to place that script inside an DIV and add runat="server with some ID in Master Page Form control.
<div id = "dvScript" runat = "server">
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
<script type="text/javascript">
function ShowProgress() {
setTimeout(function () {
var modal = $('<div />');
modal.addClass("modal");
$('body').append(modal);
var loading = $(".loading");
loading.show();
var top = Math.max($(window).height() / 2 - loading[0].offsetHeight / 2, 0);
var left = Math.max($(window).width() / 2 - loading[0].offsetWidth / 2, 0);
loading.css({ top: top, left: left });
}, 200);
}
$('form').live("submit", function () {
ShowProgress();
});
</script>
</div>
And then in content page's Page Load event write following code to disable the script.
this.Page.Master.FindControl("dvScript").Visible = false;