The method you want is Session.Close
And yes, user2864740 is quite correct: you must explicitly set the object to Nothing.
Further, I would recommend that you close each and every every object created by Session, setting them to Nothing, too: you should never assume that any object has been dismissed and cleaned-up when it goes out of scope - and if any one of them is left alive, it can keep a reference to the parent object, keeping the session alive and inaccessible to your attempts to close it.
If you haven't explicitly closed the session, and it's still open after you've ditched every object variable that pointed to it, it's probably out of reach of VBA.
There are some objects that can be picked up by a GetObject() call if they are already running, but the Lotus Notes Session object doesn't support that interface.
Your next step would be to use API calls to enumerate the running processes, pick out the Lotus Notes Session PID by name, and kill the process
An alternative to using 'Process' API calls is WMI scripting, and MSDN have a VBScript listing for the relevant calls here:
https://msdn.microsoft.com/en-us/library/aa394599%28v=vs.85%29.aspx
This is safer than the API calls, but you should still regard this as a last resort: it will probably kill your existing mail session and there's a reason why Task Manager (your UI for enumerating processes and killing PIDs) gives you warnings about unsaved work and system instability.