Upload patches/bundles (a ZIP file named something like ESXi500-201109001.zip) to a datastore visible to the ESXi server that you want to update. Not all bundles requires the server to be in maintenance mode, but some do. I recommend that you migrate any running machines away and enter maintenance mode. Now SSH into you’re ESXi server and execute the following command (with the datastore-name and bundle-name replaced).
# esxcli software vib install -d /vmfs/volumes/datastore-name/bundle-name.zip