Does Microsoft releases patches/version upgrades for SCOM Agent specifically or is it only part of SCOM CU rollup?

I want to use SCCM to roll out patches for SCOM Agent on all the servers which we are monitoring. Can we do it?

Sorry, I think I have misunderstood your question.

Ordinarily, Microsoft recommend that you install the update rollup package by following these steps in the given order:

1. Install the update rollup package on the following server infrastructure:

   •Management servers

   •Gateway servers

   •Web Console Server role computers

   •Operations Console role computers

2. Apply SQL scripts.

3. Manually import the management packs.

4. Apply the agent update to manually installed agents, or push the installation from the Pending view in the Operations console.

Meanwhile, this is a separate KB for Microsoft Monitoring Agent (KB 3165492)

You could deploy the SCOM agent by SCCM.

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Yes. You need to push the SCCM agent to the servers.

There are 2 ways to deploy software updates using SCCM 2012 R2, Manual and Automatic. In Manual software updates deployment, a set of software updates is selected the Configuration Manager console and these updates are deployed to the target collection whereas Automatic software updates deployment is configured by using automatic deployment rules. When the rule runs, the software updates that meet a specified criteria are added to a software update group, the content files for the software updates are downloaded and copied to distribution points, and the software updates are deployed to client computers in the target collection.

For a complete description of the steps mentioned above, check out the articles below:

Introduction to Software Updates in Configuration Manager

How To Deploy Software Updates Using SCCM 2012 R2