You are correct that traditional Auto Scaling launches a new Amazon EC2 instance, and then associates that EC2 instances with the Load Balancer on a single port.
In a Microservice environment (where there are multiple services on each instance, each operating behind a different port), it is recommended to use the Amazon EC2 Container Service that manages the deployment of containers across multiple EC2 instances.
The Amazon EC2 Container Service also features Service Auto Scaling, which can automatically deploy new containers based upon metric thresholds. This is, effectively, the same as traditional Auto Scaling but at the Container level rather than the Instance level.
When adding new containers, it should be able to add the new containers to the Application Load Balancer. (I haven't tried it myself, but that's the theory!)