First possibility
You have some options outside Jsoup, i.e. employing a "real" browser and interact with it. An excellent choice for this would be selenium webdriver. With selenium you can use different browsers as back end, and maybe in your case the very lightweight htmlUnit would do already. If more complicated JavaScript is called there is often no other choice then running a full browser. Luckily, phantomjs is out there and its footprint is not too bad (headless and all).
Second possibility
Another approach could be that you grab the javascript source with JSoup and start a JavaScript interpreter within Java. For that you could use Rhino. However, if you go that path you might as well use HtmlUnit directly, which is probably a bit less bulky.
