nbstripout [1] is my favorite tool for this. Installing it in your Git repo is 2 lines:

$ pip install --upgrade nbstripout # install nbstripout bin

$ nbstripout --install # install Git hook in current repo

Then, any .ipynb files that you check in will have their output stripped in the index (without affecting your working copy).

(Surprised it's not mentioned in the article.)

[1] https://github.com/kynan/nbstripout