How to remove a container that is attached to the body

Make your containervar point to a jq object instead of a string:

var container = $('<div class="foo"> ... </div>');

// Prepend it to the body
$("body").prepend(container);

setTimeout(function() {
   container.fadeOut();
}, 3000);

Now, instead of a silly string , containerthere's a method.fadeOut()

EDIT: Per request, the original version of the creation section:

var container = document.createElement("div");
container.className="foo";
container.innerHTML= "<b>Hello world</b>";
document.body.insertBefore(container, document.body.firstChild);

The fadeOut part in vanilla:

<style> 
        div.foo{ opacity: 1; transition: 1000ms opacity;}
        div.foo.fade { opacity: 0; }
</style>

  setTimeout(function(){ container.classList.add("fade");}, 3000);