How about using display:none for 2 seconds like this:
document.getElementById("restart").onclick=function(){
document.getElementById("restart").style.display = 'none';
new = setTimeout(function() {
restartGame();
}, 2000);
clearTimeout(new); clearTimeout(timer); restartGame(); };
Then when restartGame() is called after the 2 second setTimeout delay, make it reappear using document.getElementById("restart").style.display = 'inline';