Yes, you can do this with AWS Systems manager. AWS Systems Manager Run Command allows you to remotely and securely run set of commands on EC2 as well on-premise server. Below are high-level steps to achieve this.
Attach Instance IAM role:
The ec2 instance must have IAM role with policy AmazonSSMFullAccess. This role enables the instance to communicate with the Systems Manager API.
Install SSM Agent:
The EC2 instance must have SSM agent installed on it. The SSM Agent process the run command requests & configure the instance as per command.
Execute command :
Example usage via AWS CLI:
Execute the following command to retrieve the services running on the instance. Replace Instance-ID with ec2 instance id.
aws ssm send-command --document-name "AWS-RunShellScript" --comment "listing services" --instance-ids "Instance-ID" --parameters commands="service --status-all" --region us-west-2 --output text
More detailed information: https://www.justdocloud.com/2018/04/01/run-commands-remotely-ec2-instances/