Fading an element in from display: none; with CSS transitions.

box.css

.box {
	display: block;
	background: red;
	width: 200px;
	height: 200px;
	opacity: 1;
}

.box-hidden {
	display: none;
}

/* ensure box is displayed block during the transition  */
.box-transition.box-hidden {
	display: block;
	opacity: 0;
}

.box-transition {
	transition: opacity 1s ease;
}

box.html

<div class="box">
</div>
<button class="button">Toggle Box</button>

box.js

document.addEventListener('DOMContentLoaded', function() {
	var box = document.getElementsByClassName('box')[0],
	    button = document.getElementsByClassName('button')[0];

	button.addEventListener('click', function(e) {
		if (box.classList.contains('box-hidden')) {
			// show
			box.classList.add('box-transition');
			box.clientWidth; // force layout to ensure the now display: block and opacity: 0 values are taken into account when the CSS transition starts.
			box.classList.remove('box-hidden');
		} else {
			// hide
			box.classList.add('box-transition');
			box.classList.add('box-hidden');
		}
	}, false);

	box.addEventListener('transitionend', function() {
		box.classList.remove('box-transition');
	}, false);
});

I finally managed to change the script so that the box is hidden at start and then displayed on click of the toggle button.

HTML

<div class="box">
</div>
<button class="button">Toggle Box</button>

CSS

.box {
  display: none;
  background: red;
  width: 200px;
  height: 200px;
  opacity: 0;
}

.box-visible {
  display: block;
}
.box-active {
  display: block;
  opacity: 1;
}
.box-transition.box-visible {
  display: block;
  opacity: 1;
}
.box-transition {
  transition: opacity 0.5s ease;
}
.box-hidden {
  display: block;
  opacity: 0;
}

JavaScript

document.addEventListener("DOMContentLoaded", function () {
    var box = document.querySelector(".box"),
    button = document.querySelector(".button");

  button.addEventListener(
    "click",
    function (e) {
      if (box.classList.contains("box-active")) {
        // hide
        box.classList.remove("box-active");
        box.classList.add("box-transition");
        box.classList.add("box-hidden");
      } else {
        // show
        box.classList.add("box-visible");
        box.clientWidth;
        box.classList.add("box-transition");
        box.classList.add("box-active");
      }
    },
    false
  );

  box.addEventListener(
    "transitionend",
    function () {
      box.classList.remove("box-transition");
      box.classList.remove("box-visible");
      box.classList.remove("box-hidden");
    },
    false
  );
});

Not sure whether this is efficient way to do it but it works.