That's what I wanted!

You can do this by editing the extension's manifest.json file:

• On Windows: C:\Users\<USERNAME>\AppData\Local\Google\Chrome\User Data\Default\Extensions\<EXTENSION-ID>\<VERSION>\manifest.json (find out the extension's ID by enabling Developer Mode in the extension settings page)

• On MacOS: Open /Users/USERNAME/Library/Application Support/Google/Chrome/Default/Extensions/EXTENSION-ID/VERSION/manifest.json in a text editor.

• On Ubuntu for Chromium: ${HOME}/.config/chromium/Default/Preferences

In this file, set the "update_url" property to something invalid like "https://localhost" for example. For the given url, it makes auto-updating that extension as simply impossible.

Source: https://productforums.google.com/d/msg/chrome/l3zOZeO-5-M/Y7VaR0KCWNIJ