The boto.manage.cmdshell module can be used to do this. To use it, you must have the paramiko package installed. A simple example of it's use:
import boto.ec2
from boto.manage.cmdshell import sshclient_from_instance
# Connect to your region of choice
conn = boto.ec2.connect_to_region('us-west-2')
# Find the instance object related to my instanceId
instance = conn.get_all_instances(['i-12345678'])[0].instances[0]
# Create an SSH client for our instance
# key_path is the path to the SSH private key associated with instance
# user_name is the user to login as on the instance (e.g. ubuntu, ec2-user, etc.)
ssh_client = sshclient_from_instance(instance,
'<path to SSH keyfile>',
user_name='ec2-user')
# Run the command. Returns a tuple consisting of:
# The integer status of the command
# A string containing the output of the command
# A string containing the stderr output of the command
status, stdout, stderr = ssh_client.run('ls -al')