Use JGit with the Apache HTTP client (instead of the JVM's HTTP client). This has some additional features (most notably ability to control repository authentication at project level from Jenkins), eliminates the need of installing Git client and is not subject to the forced NTLM automatic authentication using the identity of the process on Windows.

In other words, if you find the default JGit implementation doesn't appear to use the configured credentials when connecting to a Git repository on a Windows server (such as with Team Foundation Server), try this implementation.

This is still a work in progress and some features might be incomplete.