When you use our VPNGUI app in WEB mode (as opposed to OpenVPN mode) most command-line utilities, including Git, will not use the VPN automatically.
Fortunately, when using VPNGUI in WEB mode, it runs a local proxy server that many command-line utilities can use. This proxy runs a 127.0.0.1:16005.
To instruction Git to use the local proxy provided by VPNGUI you may issue this command:
git config --global http.proxy http://127.0.0.1:16005
To use Git without VPN, you will have to remove the proxy from its config again:
git config --global --unset http.proxy