How do I install a Device Agent automatically using Microsoft Azure Intune?

Deployment via Microsoft Azure Intune is supported natively using the MSI package and the
concept of line-of-business apps (Windows MSI) within Intune.

This is how you proceed with the installation:  

Setup in Security Center

1. Log in to the Security Center.
2. Click on Asset Manager.
3. Click Devices.
4. Click +New device.
5. Click Deployment:
   
   • Package: Click on the download icon to download the Device Agent installer.
   • Choose your previously created token under Tokens.
6. Copy the installation command and argument. Remove the command msiexec, MSI package
   name, and the "/i" argument to make it compatible with Intune. Example:
   
7. (Optional) Confirm if you need to use a proxy. If needed you will need to add that as an argument to the installation arguments with a proper endpoint.

Setup in Microsoft Azure Intune

Browse to Apps in your Microsoft Endpoint Manager admin center.

1.  Add a new Windows line-of-business app.
2.  Upload the MSI of Device Agent as the selected file for the app.
3. App install context is required to be Device.
4. Ignore app version set to Yes (as Device Agent is updated automatically).
5. Command-line arguments – here, you paste in the created arguments from step 6.
6. The rest of the options are custom and not a direct requirement for the installation.
7. Proceed with selecting what device groups that should receive the app.
8. Monitor the rollout of apps and confirm that it is installed successfully on all devices. Example:
   

9. Done!