To manually update EC2 instances managed by Elastic Beanstalk, you can run the following command:
For Amazon Linux 2013.09 "sudo yum install -y http://packages.us-east-1.amazonaws.com/2013.09/updates/556c...
For Amazon Linux 2014.03 "sudo yum install -y http://packages.us-east-1.amazonaws.com/2014.03/updates/e10f...