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Workaround - how to create an access token:
First, go to https://github.yourdomain.com/settings/applications/new to register a new OAuth Application on your GitHub Enterprise instance. Name it something like "Jenkins GitHub Pull Request Builder", and leave the Main URL and Redirect URL blank.
Next, request an access token with:
curl -u 'username:password' -d '{"scopes":["repo"],"note":"Jenkins GitHub Pull Request Builder"}' https://github.yourdomain.com/api/v3/authorizations
Verify this worked by visiting https://github.yourdomain.com/settings/applications/ and noting that there is a new entry under "Authorized applications"
Finally, go to your Jenkins instance and paste in the access token you got, e.g. at http://yourdomain.com/jenkins/configure under the Github pull requests builder section under Advanced...
To verify it is working, set up a pull request based trigger with a rapid trigger rate (e.g. */1 * * * * - just for testing purposes!) and watch the jenkins log, e.g.
tail -f /var/log/jenkins/jenkins.log