After Upgrade to 2016, SQL Server Agent can't connect to Instance
Problem resolved by adding an alias to the instance in the SQL Server Agent Configuration. 

The alias was defined using the fully qualified domain name of the server. Example:servername.domain.biz\instance_name otherwise the agent will still error out and shutdown.



Also, the Agent was disabled in sp_configure

sp_configure 'Agent XPs', 1
go

reconfigure with override
go


So reenabled it.