If you can run PHP from the command-line, you could probably create a script that loads the C5 environment and then copy/paste the contents of the C5 "tools" file that runs the job (maybe convert the $_GET arguments to command line parameters, and possibly make some other changes?).

Maybe this addon will work for you:
http://www.concrete5.org/marketplace/addons/nontab-scheduler/...

If not, I think you'll need to create a PHP command line script -- piece together the functionality from /concrete/dispatcher.php and /concrete/tools/jobs.php (and change the $_GET stuff to command-line parameters). If you go this route, it might be helpful to see how the command-line installer does its thing:
https://github.com/concrete5/concrete5-cli/blob/master/install-concr...