There are two ways in conjunction to patch the ESXI. First one leveraging VMware Update Manager which is best option to choose if you have bunch ESXIs in multiple cluster. You could take advantages to centralize the stage of patch including for remediation process.
Second one is over SSH but you have to do it manually:
- Copy the .zip patch file into desire datastore (preferably internal datastore)
- Execute following command “esxcli software vib update -d “/vmfs/volumes/Datastore/DirectoryName/PatchName.zip”
Once done you will have a notice to reboot the machine to apply the patch. Ensure you have the console access just in case machine does not come up post patching activity.