I was unable to get this to work within the Karma test runner, however this became significantly easier within the protractor test suite.
To accomplish this within the protractor test suite I used the following to select the first select2 box on the page and select the first option within that box:
var select2 = element(by.css('div#s2id_autogen1'));
select2.click();
var lis = element.all(by.css('li.select2-results-dept-0'));
lis.then(function(li) {
li[0].click();
});
The next select2 on the page has an id of s2id_autogen3