Q. How can I manage Azure VMs from System Center Virtual Machine Manager 2012 R2?
A. Update Rollup 6 (UR6) for System Center Virtual Machine Manager (SCVMM) 2012 R2 introduces the ability for limited management of VMs in Azure. Once UR6 for SCVMM 2012 R2 is installed (it's available here) you can add Azure subscriptions to the SCVMM console. You'll need a management certificate that is associated with the subscription, the subscription ID, and a name. Note that at this time UR6 does not support Azure AD authentication to the subscription.
Once the subscription is added, the VMs will be displayed as shown and you can perform basic management such as start, stop, shutdown, restart and connect via RDP.