You can use
overflow-y: auto
This makes the scrollbar only visible when it is needed.
Updated FIDDLE
UPDATE:
You can also just make the content of the popup scrollable so the titlebar remains in view:
#confirmDialog .ui-content {
overflow-y: auto;
}
$('#confirmDialog').on({
popupbeforeposition: function() {
var maxHeight = $(window).height() - 120;
$('#confirmDialog .ui-content').height(maxHeight);
}
});