First of all you need the following article
Basically because you can now assign usb devices to VMs, you need to stop the service that does so
/etc/init.d/usbarbitrator stop
You will then be able to find the usb under /vmfs/volumes after you reconnect it. You don't need to restart the service as you will reboot after the updates
Now put your ESXi in maintenance mode
vim-cmd hostsvc/maintenance_mode_enter
Then to apply patches, use the following command
esxcli software vib install -d /vmfs/volumes/[USB]/[PATCH_FILE].zip
For more information go to http://www.chriscolotti.us/vmware/vsphere/how-to-patch-vsphere-5-esxi-without-update-manager/
Reboot when done and you should be setup!