Update Manager with vSphere is the preferred method. However, this can be done via the SSH command line in ESXi 5.
First, you will want to upload the zip patches needed to the local datastore.
Second, navigate to the host configuration tab. Then to the Security Profile. Under Services, click the properties link. Highlight SSH and click the Options button. Click Start and then OK out of the window.
Now you can SSH to the ESXi 5 host. If your patch was ESXi500-201109001.zip uploaded to datastore1 the command would be something like:
esxcli software vib update --depot=/vmfs/volumes/datastore1/ESXi500-201109001.zip
There is a lot of information on this at http://communities.vmware.com/people/vmroyale/blog/2011/09/15/updating-esxi-5--single-use-esxcli-how-to. You don't need to use the vCLI though, the esxcli command should be available in SSH.