How can I pause setInterval() functions?

You shouldn't measure time in interval function. Instead just save time when timer was started and measure difference when timer was stopped/paused. Use setInterval only to update displayed value. So there is no need to pause timer and you will get best possible accuracy in this way.

You could use a flag to keep track of the status:

var output = $('h1');
var isPaused = false;
var time = 0;
var t = window.setInterval(function() {
  if(!isPaused) {
    time++;
    output.text("Seconds: " + time);
  }
}, 1000);

//with jquery
$('.pause').on('click', function(e) {
  e.preventDefault();
  isPaused = true;
});

$('.play').on('click', function(e) {
  e.preventDefault();
  isPaused = false;
});

h1 {
    font-family: Helvetica, Verdana, sans-serif;
    font-size: 12px;
}

<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
<h1>Seconds: 0</h1>
<button class="play">Play</button>
<button class="pause">Pause</button>

This is just what I would do, I'm not sure if you can actually pause the setInterval.

Note: This system is easy and works pretty well for applications that don't require a high level of precision, but it won't consider the time elapsed in between ticks: if you click pause after half a second and later click play your time will be off by half a second.