I think this does what you're asking for:
window.onscroll = function () {
var i = 0;
var elements = document.getElementsByClassName("container");
for(var j=elements.length-1; j>0; j--)
{
if (parseInt(elements[j].getBoundingClientRect().top) <= 0)
{
i = j;
break;
}
}
var nav = document.getElementsByClassName("nav");
for (var j=0; j<nav.length; j++)
nav[j].style.backgroundColor = "";
nav[i].style.backgroundColor = window.getComputedStyle(elements[i]).getPropertyValue("background-color");
}
window.onscroll();
Here's a demo on JSFiddle.
Doing it in pure JavaScript was quite fun :D