Modifying your /system partition in Android requires root. It's nothing more than executing the su command, which then gives you the opportunity to push files onto the partition, among other things. Users with root access should be extremely careful, as it's relatively easy to soft brick a device and/or cause boot loops. There are a few applications that broker root access and a hefty number of apps that require such access to work.

Root is necessary to back up /data, modify some kernel values, and so on. But how do you prevent applications from gaining root even when auto grant is activated? The answer comes in the form of an Xposed Framework module.

XDA Forum Member devadvance created a module that can prevent shell access from being visible to certain applications. This solution allows you to keep your favorite SuperSU or Superuser settings and control other apps available on your device. There is even a possibility to block the su library for root applications, but you need to keep in mind that you will lose root access if you decide to test it. The developer provided a list of popular applications that have been tested, with root hidden successfully.

This module can be downloaded from the development thread or straight from Xposed database. Your device must be rooted and have Xposed installed, but you already knew that.