There are three ways to open a tooltip. You can see them under the "How to use" tab on page Javascript tooltip.
To make the tooltip search engine friendly, you need to take the second or third approach.
Using the second apporach:
As the content is contained within the id="contentElementId" element, the content will be crawled and indexed by search bot such as Goolge, Bing.
For example:
<a class="tooltip" href="tooltip/src/tooltip-ajax.html"
onmouseover="tooltip.ajax(this, 'tooltip/src/tooltip-ajax.html#div2');"
onclick="return false;">triggered by Hijax link</a>