[Sweet]

Типа того?

<div id="timer">0</div>
<input type="button" id="bttn" value="confirm">
<script>

var timer = 0,
    div = document.getElementById("timer");

setInterval(function(){
  div.innerHTML = ++timer;
}, 1000);

document.getElementById("bttn").onclick = function(){
  var time = new Date;
  confirm("...");
  timer += Math.round( ( new Date - time ) / 1000 );
  div.innerHTML = timer;
};
</script>