How do I fix the deprecation warning that comes with pylab.pause?

Use the warnings module. https://pymotw.com/2/warnings/

import warnings
..
..
warnings.filterwarnings("ignore",".*GUI is implemented.*")

This looks for the pattern 'Gui is implemented' in any warning being issued and ignores it but allows other warnings to be reported.

It seems it has been fixed in matplotlib thus updating the lib should work

pip install --upgrade matplotlib