Since you cannot have Defender update itself automatically while auto-install all updates is off, you could click the security center alert and select check for definitions, which would pop-up the defender window and show you the updating progress etc.
With a little procmon tracing it turns out that the security center is calling the following command:
"%programfiles%\MpCmdRun.exe" SignaturesUpdateService -UnmanagedUpdate
which in turn forces a manual update of the definitions if any update is available and most importantly does not open the main defender window or interact with the desktop so you can have it completely automated as a daily scheduled task or a log-on script for example.
Command might need administrative privileges. I could not find this command documented in the command-line switches.
Listing the command-line parameters of MpCmdRun we can see another possibility which is
"%programfiles%\Windows Defender\MpCmdRun.exe" SignatureUpdateso you might have luck with that one.