In my humble opinion, the most effective way to achieve this is by utilizing LESS. By creating a theme.less file and incorporating all the original Bootstrap files you desire, along with your own custom overrides in the same file, you can streamline the process. Detailed instructions for this technique can be found in this helpful tutorial.
The advantage of using LESS is that it compiles into a single CSS file, simplifying the minification process in your current setup. Additionally, this method enables you to work independently from the original Bootstrap files, allowing for seamless updates without complications down the line.
Alternatively, if you only have one CSS rule to modify, consider adjusting your grunt installation to combine a small CSS file containing your custom rule(s) with your main.css file and minify them together. This can be achieved through the configuration provided in the cssmin plugin documentation here. Alternatively, you could opt for the user-friendly approach of using Brunch (it's much simpler! :-)