System Center Configuration Manager current branch (version 1610) has added support for macOS Sierra (v10.12). Configuration Manager Mac clients should have a minimum client version of 5.0.8466.1 to support macOS Sierra. Find information about how to upgrade the Configuration Manager Mac client here.
Microsoft has also released an update to System Center Endpoint Protection (SCEP) for Mac which includes support for macOS Sierra. It is available on the Volume Licensing Service Center (VLSC). You can download the latest Mac client for System Center Configuration Manager here.