CSS Auto hide elements after 5 seconds

YES!

But you can't do it in the way you may immediately think, because you cant animate or create a transition around the properties you'd otherwise rely on (e.g. display, or changing dimensions and setting to overflow:hidden) in order to correctly hide the element and prevent it from taking up visible space.

Therefore, create an animation for the elements in question, and simply toggle visibility:hidden; after 5 seconds, whilst also setting height and width to zero to prevent the element from still occupying space in the DOM flow.

FIDDLE

CSS

html, body {
    height:100%;
    width:100%;
    margin:0;
    padding:0;
}
#hideMe {
    -moz-animation: cssAnimation 0s ease-in 5s forwards;
    /* Firefox */
    -webkit-animation: cssAnimation 0s ease-in 5s forwards;
    /* Safari and Chrome */
    -o-animation: cssAnimation 0s ease-in 5s forwards;
    /* Opera */
    animation: cssAnimation 0s ease-in 5s forwards;
    -webkit-animation-fill-mode: forwards;
    animation-fill-mode: forwards;
}
@keyframes cssAnimation {
    to {
        width:0;
        height:0;
        overflow:hidden;
    }
}
@-webkit-keyframes cssAnimation {
    to {
        width:0;
        height:0;
        visibility:hidden;
    }
}

HTML

<div id='hideMe'>Wait for it...</div>

based from the answer of @SW4, you could also add a little animation at the end.

body > div{
    border:1px solid grey;
}
html, body, #container {
    height:100%;
    width:100%;
    margin:0;
    padding:0;
}
#container {
    overflow:hidden;
    position:relative;
}
#hideMe {
    -webkit-animation: cssAnimation 5s forwards; 
    animation: cssAnimation 5s forwards;
}
@keyframes cssAnimation {
    0%   {opacity: 1;}
    90%  {opacity: 1;}
    100% {opacity: 0;}
}
@-webkit-keyframes cssAnimation {
    0%   {opacity: 1;}
    90%  {opacity: 1;}
    100% {opacity: 0;}
}

<div>
<div id='container'>
    <div id='hideMe'>Wait for it...</div>
</div>
</div>

Making the remaining 0.5 seconds to animate the opacity attribute. Just make sure to do the math if you're changing the length, in this case, 90% of 5 seconds leaves us 0.5 seconds to animate the opacity.

Of course you can, just use setTimeout to change a class or something to trigger the transition.

HTML:

<p id="aap">OHAI!</p>

CSS:

p {
    opacity:1;
    transition:opacity 500ms;
}
p.waa {
    opacity:0;
}

JS to run on load or DOMContentReady:

setTimeout(function(){
    document.getElementById('aap').className = 'waa';
}, 5000);

Example fiddle here.