I think this does the job:
gnome-session-save --logout
Also, take a look at the --help output, maybe you want to use the --force-logout option.
Usage:
gnome-session-save [OPTION...]
Help Options:
-h, --help Show help options
--help-all Show all help options
--help-gtk Show GTK+ Options
Application Options:
--logout Log out
--force-logout Log out, ignoring any existing inhibitors
--logout-dialog Show logout dialog
--shutdown-dialog Show shutdown dialog
--gui Use dialog boxes for errors
--display=DISPLAY X display to use