Eric,

You should be able to curl it down.

1. First find out the URL of the package you want to download,
   curl -s $(strings /System/Library/PrivateFrameworks/SoftwareUpdate.framework/SoftwareUpdate | awk '/https/ && /sucatalog/') | awk '/[Update name without the brackets]/ && /pkg/'

e.g. curl -s $(strings /System/Library/PrivateFrameworks/SoftwareUpdate.framework/SoftwareUpdate | awk '/https/ && /sucatalog/') | awk '/2016-003/ && /pkg/'

1. Once you have the appropriate URL, use curl to down the package,
   curl -O [proper above URL]

e.g. curl -O http://swcdn.apple.com/content/downloads/63/05/031-78817/kq8igkg4q86t4bb820apbkszfxy5dlywwe/SecUpd2016-003ElCapitan.pkg

Good luck,
jkb

I got it today, on a 10.11 machine by running

sudo softwareupdate -d Security Update 2016-003-10.11.6

Then find the package in /Library/Updates

Depending upon Mac model, there are Firmware updates that are installed. The GUI does not appear to display the familiar notice though. I'm using caution on this one, several test Macs behaved oddly.

@jkb Thanks for the command. I'll have to remember that for next time. I took the easy way and waited for the AutoDMG UpdateProfiles.plist to be updated, and looked within it to find the URL: http://swcdn.apple.com/content/downloads/63/05/031-78817/kq8igkg4q86t4bb820apbkszfxy5dlywwe/SecUpd2016-003ElCapitan.pkg (as you had already included above).

Thanks for the responses everyone. I found the update (well, really updates) on my NetSUS as well, but the problem is that there are three pkgs that are part of this one update (031-78817):
http://swcdn.apple.com/content/downloads/63/05/031-78817/kq8igkg4q86t4bb820apbkszfxy5dlywwe/SecUpd2016-003ElCapitan.pkg
http://swcdn.apple.com/content/downloads/63/05/031-78817/kq8igkg4q86t4bb820apbkszfxy5dlywwe/FullBundleUpdate.pkg
http://swcdn.apple.com/content/downloads/63/05/031-78817/kq8igkg4q86t4bb820apbkszfxy5dlywwe/FirmwareUpdate.pkg

As @bainter mentioned, what is installed depends on the model of Mac and probably some other factors. I tried the method mentioned by @dpertschi and only got two of the three packages listed above: the FullBundleUpdate.pkg is missing. There is a .dist file, but I'm not able to fully decipher it.

Bottom line, I don't know what method Apple is using to bundle these together and make sure the right packages are installed. That's why I went to the support downloads site to grab the usual DMG that contains a single package. I thought maybe the FullBundleUpdate.pkg would be the ticket, but it's the smallest of the three by a long shot, so there's no way it contains everything needed.

Thanks,
Eric

Hi,

Here is the link from Apple KB :

https://support.apple.com/kb/DL1903?locale=en_US

Yay, looks like they finally realized they had forgotten to post it! Thanks, @tomgi !