I'm not familiar with Python or Pywikibot but believe it could do this easily. A script passed three command-line arguments (article name, edit summary, local filename) replaces the article with the contents of local filename. Just uploads new wiki-source overwriting the existing article.
I tried something like this but it didn't work
import pywikibot, sys
- Usage: savepage [article name] [edit comment] [local file]
f = open(sys.argv[3], 'r')
newtext = f.read()
site = pywikibot.Site('en', 'wikipedia')
page = pywikibot.Page(site, sys.argv[1])
page.text = newtext
page.save(sys.argv[2])