How can I create a patch for a contrib module or core which is not in version control?
So, you would have to download the module seperately, like:

git clone --branch 8.1.x http://git.drupal.org/project/colorbox.git


Then, you make the change and run the following:

git diff 8.1.x &gt; colorbox-css-issue.patch


This creates a patch for this module. Now you can place the patch in a patches folder and add it to your composer.json file.
Helpful source: https://www.drupal.org/node/707484