setTimeout does not pause; it asks Javascript to run some other code later.
Googling for "setTimeout loop" tells you exactly what you need to know. If you look around a little bit, it even mentions setInterval. The difference: using setTimeout to loop will wait 3 seconds in between loops, whereas setInterval will make it take 3 seconds total for the loop (including however much time the animation takes, as long as it's less than 3 seconds :) ). Also, setInterval constructs an infinite loop that you'll have to break out of after the desired number of times; setTimeout requires you to construct the loop yourself.
i = 0;
// setTimeout approach
function animation_loop() {
  someAnimation();
  setTimeout(function() {
    i++;
    if (i < n) {
      animation_loop();
    }
  }, 3000);
};
animation_loop();
// setInterval approach
i = 0;
someAnimation();
iid = setInterval(function() {
  i++;
  if (i < n) {
    someAnimation();
  } else {
    clearInterval(iid);
  }
}, 3000);