WIX provides a Custom Action that allows to run Command line silently - Quiet Execution Custom Action
You should use it exactly the same way as listed in the WIX example. Just put your command in the Properties value.
<Property Id="QtExecCmdLine" Value='"command" parameters'/><CustomAction Id="QtExecExample" BinaryKey="WixCA" DllEntry="CAQuietExec" Execute="immediate" Return="check"/>
Make sure the command has double quotes. For example: '"ping" -n 15 127.0.0.1'
Don't forget to add the WixUtilExtension extension during building the msi package.