Edit in JSFiddle

window.onload = function()
{
    var map = new ymaps.Map("ymaps-map", {center: [37.49966065266167, 55.742409980028505], zoom: 16, type: "yandex#map"});
    $('#ymaps-map').html('');
    setTimeout(function() {
        map.destroy();
    }, 2000);
};

<div class="yandexMap" id="ymaps-map" style="width: 600px; height: 376px;"></div>