There are a number of ways this can be accomplished. If you have SDSF at your site you could issue the MVS command using SDSF in batch as you would do from the SDSF screen. As long as the ID issuing the command has authority to do so. JES2 and JES3 also have ability to issue MVS commands.
I believe you could use IKJEFT01,IKJEFT1A, or IKJEFT1b and issue a CONSOLE command but you would need to talk to your system programmers to see how to make the session you start with those authorized.
I have not used this method but this if from the IBM manual:
COMMAND Statement
z/OS V1R9.0 MVS JCL Reference
SA22-7597-11
Purpose
Use the COMMAND statement to specify an MVS™ or JES command that the system issues when the submitted JCL is converted.
The COMMAND statement is the preferred way within the job control language to specify commands, rather than using the JCL command statement, which is described in JCL Command Statement. That is because the COMMAND statement is in standard JCL statement format, is parsed and processed using code common to the other JCL statements, and if necessary may be continued across multiple card images, that is, is not limited to 80 characters. Note that some MVS subsystems, including TSO, JES2, and JES3, offer additional ways to enter system commands outside JCL, which may be preferable under certain circumstances.
When the system encounters an in-stream command it issues message IEFC165I to inform the operator. If the operator is requested to authorize running of commands entered through the input stream, the system then issues message IEFC166D asking for the operator to respond. The operator should respond REPLY id,'Y' if the command displayed in message IEFC165I is to be run, and REPLY id,'N' otherwise.
Because the system usually executes an in-stream command as soon as it is converted, execution of the command will not be synchronized with the execution of any job or job step in the input stream. To synchronize a command with job processing, tell the operator the commands you want entered and when they should be issued, and let the operator enter them from the console.
The system processes each command according to installation options for both the input device from which the job was read, and the job class.
On a JES3 system, the system does not record in a job's JESMSGLG data set any commands you enter with the COMMAND statement.
References
For more information on MVS and JES commands and for descriptions of their parameters, see z/OS MVS System Commandsz/OS MVS System Commands, z/OS JES2 Commands, and z/OS JES3 Commands.
Considerations for an APPC Scheduling Environment
The COMMAND statement has no function in an APPC scheduling environment. If you code a COMMAND statement, the system will check it for syntax and then ignore it.
I hope this helps. I am sure there are other ways to issue MVS commands such as IOF if you have that in your shop...etc
I have also seen where you can issue a "command" to your MVS automation software (MVSOPS...etc) and have that issue the appropriate MVS command.