I slightly updated your demo at and have set transition time to 1000ms to easier recognise the animation. Tooltip fade in and fade out - it works for me:

enter image description here

Did not changed much, but removed the 'instant pop up' at mouseover:

      .on("mouseover", function(v) {
                  .duration(1000) //longer to easier be seen
                  .style("opacity", 0.9); //this is for the tooltip
              var text = "Alert<br/>"+ formatTime(v[0]) + "<br/>" + v[1];
                  .style("left", (d3.event.pageX)+"px")
                  .style("top", (d3.event.pageY-28) + "px")
                  .attr("fill", "steelblue");
                 // .style("opacity", 0.9); // not here

Tested on latest Desktop Browsers as Chrome 35, Safari 7 and Firefox 29. Older Opera 12 struggles with mouse over, maybe the tooltip overlays the point and therefore the mouse over does not count anymore. What browser do you use?