You should be able to use SAVSYS to take a complete backup of the system except for the user libraries and DLO objects. You will need to have the system in restricted state (no other jobs or subsystems active). I would suggest you do the following :-
Preferably from the console (otherwise use TFRJOB to transfer your interactive session into your controlling subsytem). Change QSYSOPR message queue to *BRAK mode. Issue the ENDSYS command. You should receive a break message when the system is in restricted mode (otherwise keep an eye on QSYSOPR). Start the SAVSYS command. Once the SAVSYS command is completed, restart your system with an IPL using PWRDWNSYS RESTART(*YES).
If you need backups of the user libraries and DLO’s you can do a SAVLIB *NONSYS and a SAVDLO before you restart your system.
As an alternative you can use GO SAVE then option 21 to save entire system (this does the SAVSYS, SAVLIB *NONSYS and the SAVDLO for you).